This chapter provides a quick look-up reference for selection on the X-AUTOFIT:X-BUILD palette. This palette provides the tools to generate and modify bones, skeletons and sequences.
X-AUTOFIT is accessed from the Applications menu in the QUANTA main menu:
1. Create a new directory in which to run X-AUTOFIT. Move to that directory, and start QUANTA.
2. Select X-AUTOFIT from the Applications menu. The main X-AUTOFIT:X-BUILD palette and the Pointer palette appear, as well as a graph window containing the allowed regions for a Ramachandran map, and any points representing the phi-psi angles for any known coordinates. If the map table is not open, then open it using the Map show table (select Map table | Show map table from the Draw menu) tool.
An Object Management table will also open and will fill with objects as they are generated for the following: bones, mask, symmetry atoms, Ca-trace, and 3D text.
The Object Management table can be used to toggle the relevant information on and off. Objects can be deleted from this table, but X-AUTOFIT will generate these again if required.
When you start X-AUTOFIT, the X-AUTOFIT:X-BUILD palette is displayed as illustrated, along with the Geometry palette and X-AUTOFIT dials emulator. The Ramachandran map opened is described in full in Using X-BUILD, and the Ca plot is described in Using X-AUTOFIT. The presence of these plots and how to control their use, such as switching between the different displays, is described in Graph windows.
On first use of X-AUTOFIT, if a map is currently open, then a map contoured with a radius of 9 Å will be displayed at the center of the screen display. On subsequent entry to X-AUTOFIT, you will find that any other palettes that were open on the last exit from X-AUTOFIT are also opened. Also, any other addition information such as bones, Ca trace, sequence information, etc., are displayed on the screen if they were present on exit from the last X-AUTOFIT session.
The following information is saved between X-AUTOFIT sessions and is effective on subsequent use:
The majority of the parameters described here are set up on the X-AUTOFIT | Options dialog box. For a description of these parameters refer to X-AUTOFIT Options dialog box. The memory pie chart flag and the picking radius can only be changed by editing the file xfit.pack.
This tool sets up the type of map to be calculated and also the reflection file to be used. This is based on the map calculation dialogue from the CNX interface. Note that the bottom three options should be ignored. Map calculation should always be "immediate".
This tool launches a series of calculations which result in a map being generated and displayed on screen.
The map calculation will be performed taking into account any changes in topology or conformation of the molecular system under study. See Managing Maps for more information.
The Symmetry palette allows the definition of symmetry and NCS (noncrystallographic symmetry). Several symmetry objects can be created with tools on this palette.
A separate graphical object is generated for each symmetry element, labeled with the symmetry operator. Individual symmetry objects can be toggled on or off (using the Displayed column in the Object Management table) or deleted with the Object Management table.
Each symmetry object has a different name, formed from the translation and symmetry transformation used to generate it. For example, the molecule generated by applying a unit-cell translation of 0,1,-1 in a, b, and c for symmetry operator number 3 is named S+0+1-1:3. If any noncrystallographic symmetry operator is applied, the name also includes this information in the true symmetry operator.
Symmetry atoms can be picked and the information about parent real atoms is returned along with the symmetry detail for the symmetry atom picked.
You can delete all symmetry objects by using the Delete Sym.Ob tool in the Object Management table, which deletes all graphical objects whose name starts with S and contains a colon (:). If you want to retain a particular symmetry object, change its name (using the Name cell in the Object Management table) before using Delete Sym.Ob.
Define Symmetry allows definition of the symmetry of the current molecule or can be used to change the symmetry of the current molecule. This information is not written to the MSF until X-AUTOFIT | Finish and then the new MSF files contain the new symmetry information.
1. A dialog box that prompts for either the space group number or space group name. For example, r3 is 146.
2. A dialog box for the cell dimensions. The number of lines to enter on this dialog box will depend on the point group, as some entries on cell dimensions and cell angles are degenerate. If a map is currently open, the default cell dimensions will be read from the map header, so may not need changing.
3. A dialog box for the ncode. This defines the axis order for the cell. Normally the ncode is one.
The symmetry atoms will be updated based on the new symmetry specification.
The Non Crystallographic Symmetry dialog allows the specification of the real-space rotation matrix and translation that defines the position of NCS related atoms. A dialog box appears:
Next allows the specification of further matrices.
Exit exits the NCS definition. If the current matrix is a unit matrix then this is not added.
Quit makes no change to the current NCS symmetry.
The matrix provided by the application is for the identity matrix. The values that specify the NCS should be typed into the matrix. If you do not provide a matrix with a unit value determinant you will not be allowed to enter further matrices with the Next option or to Exit. A warning appears in the textport to indicate the presence of a undefined matrix.
The NCS information is written to the key worded free format symmetry file molecule-name.sym on exit from the NCS tool editing tool. The NCS symmetry matrix is written out with a NSYM keyword and the 12 matrix values on 4 lines of the file (the first 3 on the same line as the NSYM card). It can be easier to add NCS symmetry information directly to this file as multiple NSYM cards. Some programs define the NCS information as the transpose or rotation part of the matrix depending on the internal representation. The transpose of the NCS matrix can be added to the symmetry file with the keyword NTSY.
On exit, the NCS atoms will be calculated and drawn as red (color 3) atoms. You can define up to 60 NCS matrices. To delete all the NCS, exit with unit matrix as the first matrix.
Clicking his tool generates a unit cell box. The box can be removed again by deleting the object from the object management table.
The CA-Packing Diagram tool generates a number of symmetry copies of the current visible and active molecules in the molecule management table, where the copies are shown as Ca traces. This is irrespective of the currently displayed atoms within the molecules. Each molecule is drawn a different color, using colors 1 to 14 in cycles of 14. The number of copies generated is defined as the number of generated molecules that have a centroid position within the Packing radius distance from the centroid of the active displayed molecules. A separate graphical object is created for each symmetry related molecule.
The Packing Diagram tool generates a number of symmetry copies of the current visible and active molecules in the molecule management table, where the copies are shown as all-atom representations. This is irrespective of the currently displayed atoms within the molecules. Each molecule is drawn a different color, using colors 1 to 14 in cycles of 14. The number of copies generated is defined as the number of generated molecules that have a centroid position within the Packing radius distance from the centroid of the active displayed molecules. A separate graphical object is created for each symmetry related molecule.
The ...Packing Radius is used for generation of the Ca-packing and packing diagrams and defines the number of copies to make. The number of copies generated is defined as the number of generated molecules that have a centroid position within the Packing radius distance from the centroid of the active displayed molecules.
The CA Filled Cell tool generates objects that constitute all the symmetry copies that fill the unit cell, regardless of whether the original molecule was within the unit cell (0-1,0-1,0-1). Hence for the space group r3, nine copies of Ca-traces are produced.
The Filled Cell tool generates objects that constitute all the symmetry copies that fill the unit cell, regardless of whether the original molecule was within the unit cell (0-1,0-1,0-1). Hence for the space group r3, nine copies of all-atom models are produced.
This tool deletes all symmetry objects that have been previously drawn.
This tool writes out a PDB file containing all the displayed symmetry copies.
This tool re-arranges waters, ligands, and heavy atoms based on the best non-bonded interactions, center-of-mass placement, or within a map mask.
This controls the display and positioning of the pointer. The pointer provides a visual cue for marking the location where certain commands will occur and allows you to step through a series of atoms or residues.
This turns on and off the display of the pointer, whose default appearance is a white tetrahedron in the molecule window.
The Show Ruler tool displays a ruler at the bottom of the molecule display. The ruler provides a helpful scale for experimental maps containing scant molecular data, and allows you to determine the size of structures seen in the electron density maps. The tool is a toggle, and picking the tool again will remove the ruler from the display.
The Map table tool toggles the map display. Display of the map table can also be controlled from the main menu bar or by entering MAP TABLE [ ON | OFF ] on the command line.
The Interactive contour tool opens the Interactive Contour palette, which allows you to interactively change the level at which an electron density is contoured (Interactive Contour palette).
These two tools change the modality of X-BUILD by defining whether a tool prompts you for the residues/atoms to act on, or whether a tool acts on a defined current residue. The current residue is the same as the definition for the Ramachandran highlighted value and is set by picking a displayed atom, or any place by tool defining an atom/residue.
If active residue is on, the current residue is highlighted (as well as the current atom indicated), and any subsequent tool acts on this single residue without prompting. You can change the current residue by picking any atom within a desired residue. This allows you to more easily select residues, without the prompt/select step. The aim is to make model building more efficient, but this option does generally allow only one residue to be edited at a time.
It is not possible to define selections of multiple residues (i.e., more than one active residue), because this leads to ambiguity when using some tools. To work around this, two new tools are supplied on the Structure palette allowing range and volume minimization from a single pick.
This changes the dial palette to show an xyz move dial set. Because different parts of the program assume the default mode of the dials (for example, placing Ca atoms, normal dial set, cursor mode), it is sometimes necessary to tell X-AUTOFIT which dials you wish to use. This palette option provides the dial set for the pointer movement. Selecting the pointer dials also results in the Ramachandran plot being drawn, if it is not already present.
This causes the display to center at the current pointer position. The pointer becomes the center of the display and is the center of the rotation of the display. If the map is active then the map is moved to this position. If the bones are active then these are calculated around the same point.
This tool moves the display to the next residue in the molecule. If the residue is an amino acid then the display will be centered on the Ca atom of this residue, otherwise the display will be at the first atom of the next residue. This point becomes the center of the display, and results in moving the map and recalculating the bones here. Specify the increment value for the next residue in the Options... | Next residue step value field.
The Place at previous residue tool behaves like the Place at next residue tool except it moves the center of display one (or more) residues backwards along the polypeptide chain. All components of the display, the map, bones, and symmetry where applicable, are regenerated centered on this point. Specify the increment value for the next step along the polypeptide chain in the Options... | Next residue step value field.
A dialog box prompts for an atom name, segment name, and residue number. The default values are for the first atom in the data structure. When you press OK, the center of display moves to this atom. If you press Cancel, then nothing happens.
This is only active if bones are on and displayed. When you select this tool, the program asks you to select a bones point. The selected point becomes the center of display, and results in moving the map and recalculating the bones. To abort the bones pick, select the tool again, and no movement occurs.
Prompts for an atom at which to center the display. This point becomes the center of display, and results in the moving the map and recalculating the bones. To abort the pick, select the Place using coord tool again, and no movement occurs.
A dialog box appears that allows you to enter specific x, y and z coordinates to place the pointer.
This item launches a help browser dialog which allows you to search the online HTML help documents using multiple keyword searches. The default help book is the Xfit how to, such as how to edit masks (Thesaurus.html). You can search the help page titles using a multiple keyword search which shows a subset of the available pages that include the keywords selected. This book also contains answers to frequently asked questions associated with the Ca-tracing functionality and model building features.
Type a word or multiple words separated by spaces in the search string line and press <Enter>. The large scroll list at the bottom of the dialog will show all the target hits for all the search words.
To view a help option, click the scrolling-list line that is of interest to you - the html browser opens with the help information on this topic.
The same tool can be used to browse any of the help books by picking these from the top scrolling list, so this tool can be used for general help book reading.
Puts away the Pointer palette.
The Interactive Contour palette allows you to interactively change the level at which the electron density is contoured. Only one contour level of one map is displayed while using this tool, regardless of the display status before you open this palette. By default, the first contour level is shown when the palette opens. The palette allows different contours and maps to be selected so that they can be manipulated interactively one at a time using a <SHIFT><CTRL> mouse action.
Moves to the next map (if any) in the list. The first contour level of that map is shown.
Returns to the previous map (if any) in the list. The first contour level of that map is shown.
Moves to the next contour level (if any) for the displayed map.
Moves to the previous contour level (if any) for the displayed map.
Stores your contouring changes, updates the display, and closes the palette.
Discards any changes, closes the palette, and returns to the display shown before the palette was opened.
For faster interaction, the map radius (in the X-AUTOFIT Options dialog box) should be set to a value appropriate to the computational power of your local machine. Also, since the bricked map file is read continuously during the interaction, it is better that these files be on your machine rather than accessed over a network.
You should have the map table visible when using the interactive tool, so that you can see the contour levels for all maps and levels. The map table retains the previous values until the map or contour level is actually changed when you are using the interactive tool.
The current map, contour level, and actual map contour value are displayed on the message line of the main molecule window.
The Bones palette is used for setting up the bones calculation. If the bones are turned on then all positioning of the screen origin results in the bones being calculated around this point at the current map radius.
When on, the bones are calculated about the current position. Because bones take a significant time to calculate, turning on this option slows down the display.
The Mask bones by mask toggle option automatically trims the bones that lie outside an open mask. On subsequent displays the bones outside the boundary are excluded from the display and from all calculations. This means that the mask becomes integral to the use of X-AUTOFIT and prevents the building of any structure in a region of the map that is symmetry related. This is particularly a problem when the crystallographer is first tracing a map and no symmetry atom can be generated since they have not yet been built.
When the toggle is on the bones are immediately trimmed to the boundary of the open mask, and any subsequent calculations are of trimmed bones. If the tool is then toggled off, trimmed bones are not automatically regenerated. Use one of the centering options to regenerate them if desired. If no mask is active when this tool is toggled on, trimming does not take place and an error message is written to the textport.
When the tool is off, no change is made to the bones.
This option displays a list of the currently open maps and allows you to choose the map for the bones and RSR calculations. If there is only one map, this tool does nothing. If you select quit, the map selection does not change. If you select OK, the new map is used for subsequent bones calculations and real-space refinement calculations. The newly calculated bones appear immediately.
This tool searches the entire map for the region that contains the largest amount of significantly high density. Once found, this region becomes the center of the display, and the map and bones are contoured here. Use this option when you are first looking at a new map and no coordinate information is available.
This selection sends to the textport information about the number of connected bones trees and their sizes, in percent of total bones. This data indicates the level of under-connectivity of the map. The textport also lists the number of false links, which indicates the level of over-connectivity.
This option is off by default, and bones appear partially smoothed. Use this selection to display bones as cubic spline curves that pass through map points. Each curve is one segment of the bones tree, so branch points and termini are exactly as found on the map. Intermediate points are approximated. You are only able to select those points that are actual points of the map.
You can show or hide the sidechains in the skeleton by toggling this tool. Sidechains are displayed in color 6 (default value is white). Combine this selection with scaling to observe a larger portion of the skeleton. This selection can be reversed by selecting Undo last delete.
With this selection, you can change the type of bones strand between sidechain and mainchain. When a bones section has a status change, its color changes from yellow for mainchain to white for sidechain. Use the Undo last selection to undo your last selection. If sidechains are hidden and you change a mainchain to a sidechain, the section disappears from the display.
This selection allows you to remove bones points from the bones skeleton. When you make this selection, the message prompt at the bottom of the molecule window instructs you to select a bones point by clicking with the mouse. The bones points that are deleted are multiple points that lie in a single chain extending from a branch point or terminus to another branch point or terminus. Any point selected from a section results in the entire bones section being deleted. You can undo your last selection by selecting Undo last delete.
Any recalculation of bones (for example, through changing the bones parameters or moving to a new bones box) overrides the delete modifications. Also, deleting a branch changes the smoothing function so some branch points move when a section is deleted.
This deletes one fragment of bones, where all the bones in the fragment are joined to give a single tree from the point selected. The tool activates the delete fragment action which remains active until another palette option is selected (such as Delete fragment again). To delete multiple fragments from the display, continue to pick points. The bones display is redrawn to show the deletion. The Undo last delete undoes the entire deletion process, and selecting the Undo last delete tool again removes the deleted points again.
This tool allows automatic deletion of bones by removing bones fragments by size. The tool removes the bones points on the basis of fragment size as an aid to map mask generation. All the bones fragments in the current map are calculated, and the total number of bones points is determined. The tool then removes the fragments of bones (that is, connected sections of bones points), that are smaller than the current fragment delete threshold. The initial threshold of deletion is set to 1% of the total number of bones points. Each subsequent use of the tool first doubles the threshold value and then deletes the bones based on this new threshold value. You should therefore use this tool repeatedly until a section of the map you actually wanted to keep is deleted. Then use the Undo last delete tool to reverse only the last deletion. This is probably the quickest method of deleting most of the small, unwanted parts of the bones for mask generation. The tool Reset delete all resets the threshold value to 1%.
The tool does not remove small sections of map that have no mainchain component. Use the Delete fragment tool to delete these.
The Reset delete all tool resets the threshold value for deletion to 1% for the Delete all fragments tool.
This returns the most recently deleted fragment or section of bones. Clicking this tool a second time reverses the undo operation, thereby repeating the deletion of the bones.
This tool creates a PDB file called bones.pdb containing single atoms defined by bones points and displays bones pseudo atoms from points separated by 1.2Å. These points are generated from the full bones point list by progressively deleting points until only the highest points in the bones trace are left. The output is an object in the object table and can therefore be deleted from the object table.
The bones.pdb file is a standard PDB-format file and can be used as part of a refinement procedure without restraints. This type of atom generation has been found to be a very good starting point for maximum likelihood unstrained refinement, since the atoms are already well placed.
This tool opens the Set up bones parameters dialog box. This dialog box allows you to manually set the start value for the bones calculation. When you click OK, the bones are recalculated. Recommended values are:
This opens a dialog box to change the delete value for bones trimming and the sidechain detect value. A value of 1-4 is good for the trim, and 10-30 for the sidechain detect value.
Pieces of bones smaller than the trim value are deleted. Increasing this value makes a cleaner display, but you lose detail.
The Side chain detect value is the maximum length of a branch that is classed as a sidechain. The program executes (Side chain detect)/4 calls to the detect function, which causes branches to be continually trimmed back. Increasing the Side chain detect value increases the number of sidechains detected, but results in some mainchains being classed as sidechains. Smaller values detect fewer sidechains. Recommended values are 18-20 for proteins that have more than 50 residues and a moderately connected map. You need smaller values for small peptides or where the density is badly broken. Sidechains smaller than the sidechain detect level are displayed in color 5 (default value is white).
When the Calc bones symmetry option is selected, the bones generated by symmetry are displayed. The symmetry-related bones are drawn in color 2 (default value is blue) and also are generated in a reduced representational form. Although the reduced representation of the bones is not as elegant as the real bones, this prevents overloading of the graphics with a very large symmetry-related object. The symmetry bones are provided to show mask overlaps when creating a solvent mask. For Ca tracing, the symmetry is shown more effectively by the symmetry-related Ca trace. The symmetry of the bones is not updated on a bones calculation, they are only regenerated by clicking this tool. This is because there is a significant delay (1-2 seconds for a large bones region) for the symmetry generation. Therefore, to update the symmetry-related bones, select this tool again.
The Map mask palette controls the generation of a map mask for solvent flattening. If generating the mask from bones, then use the Map mask palette options in conjunction with the Bones palette. The Map mask palette allows the generation of masks from bones and coordinates in the current map unit cell. It also allows interactive mask editing and has a progressive reduced representation form that allows the study of large masks even on low-powered systems. X-AUTOFIT currently reads all forms of O masks, (New, Old and Compressed) and writes O compressed format masks.
This calculates a mask from the current bones using a masking radius (default value is 4.0Å), defined by the option X-AUTOFIT | Map Mask | Mask delete radius. The maximum extent of the mask is defined by the displayed volume of the currently active map as set by the Map radius on the X-AUTOFIT | Options dialog box. You can edit the bones from the Bones palette, and see the symmetry overlap when the bones symmetry is on. After the mask calculation has completed, a spherical mask pointer appears that you can use to edit the mask surface.
This will calculate a solvent mask that covers all currently active and displayed coordinates using a masking radius (default value is 4.0Å), defined by the option X-AUTOFIT | Map Mask | Mask delete radius. The extent of the mask is defined by the displayed volume of the currently active map as set by the Map radius on the X-AUTOFIT:X-BUILD | Options... dialog box. If you want the mask to cover the entire map, set a large map radius before using the Calc. mask from coord option.
After the mask calculation has completed, a spherical pointer appears that you use to edit the mask surface.
This removes the mask and deletes any reference to the mask from the object table.
This tool forces the dial set to switch to mask editing mode only if a mask is present. This tool will also change the pointer to the spherical mask pointer.
This provides a pop-up box to change the value of the mask delete radius, which defines the volume about each atom coordinate or bones point for which the asymmetric unit is masked as protein. The default value is 4Å.
This tool provides an estimate of the solvent content based on the volume of the current mask, the number of symmetry and NCS operators, and the volume of the unit cell.
This changes the mask extent. If the mask pointer is moved to a region that is covered by the map (and so by the mask grid), but the mask does not cover this region, then this tool will increase the mask to cover this volume. If you use this option at the surface of an already-present mask, the mask volume will increase in size. The mask surface is recalculated as part of the process and may take between 0.1-5 seconds, depending on the extent of the mask and the system running X-AUTOFIT.
This changes the mask extent. If the pointer is moved to a region that is covered by the map (and so by the mask grid), but the mask covers this region, then this tool will decrease the mask extent so that this volume is solvent. Therefore, if you use this option at the surface of an already-present mask, the volume will decrease in size. The mask surface is recalculated as part of this process, which may take between 0.1-5 seconds, depending on the extent of the mask and the system running X-AUTOFIT.
This tool provides an automatic method to remove small regions within the mask (that is, protein) that have been flagged as solvent. Such small regions represent high resolution detail that should not be present in the mask. This tool does a void calculation on the mask grid and determines if there are any regions within the mask that are not accessible from the surface of the mask. These buried solvent regions are removed so that the points in the grid that form this void are changed to be not solvent points. The display changes to reflect the results. Depending on the size of the mask, the calculation will take between 1-20 seconds.
If a mask is very big, or the machine being used has only moderate graphics facilities, you may wish to use these two tools to adjust the number of points used to describe the surface. When the mask is first calculated, every point on the surface of the mask is shown by a point. If the resolution is decreased or increased, then 1/n of the points are randomly left in the surface, where n has a value between 1 and 10. Therefore, initially there are 1/1 points in the mask (all of them). If you decrease the resolution five times, then 1/5 of the points will remain in the surface. This reduces the interpretability of the surface, but allows the mask to be more easily manipulated, since the object is five times smaller. These commands will only affect the number of displayed points on the surface, and will have no effect on the stored mask or any calculation on the mask. You should also note that when using a reduced resolution mask surface, any re-display of the mask (such as when removing voids, add or deleting mask with the pointer), causes the distribution of points on the surface to change. This is because the points are randomly selected, and this selection will change on each calculation.
The mask currently displayed is written to disk as a compressed O format file. If the mask was read from a file, the cell and extent are determined by the original mask file. If the mask was generated in X-AUTOFIT then the cell and extent are determined by the current map and its extent.
A mask in an old or new or compressed O format file can be read into X-AUTOFIT. If no mask is present, a new object is created and displayed. If a mask exists, the mask that has been read from the file replaces the old mask. This allows existing masks to be edited.
Puts away the Map mask palette.
The Text palette controls the creation and use of annotations associated with points in the macromolecular structure. You can create and place text, delete text, and go to a text position. You can add up to 500 text notations.
When you select this tool you will be prompted for a text string (up to 80 characters long). This text appears at the current pointer position. To place text at a different position, move the pointer to that spot before creating the text.
This deletes the current text. You select the text to delete from a scrolling list of all the current text strings. Pick one string and select OK. If you pick Cancel, nothing is deleted.
This moves the current display center to the next text in the list. If the last text is the current text, you are not advanced to another string and a message prints to the text port. The display center, map, and bones are updated.
This moves the current display center to the previous text in the list. If the current text is the first text, you are not advanced to another string and a message prints to the text port. The display center, map, and bones are updated.
This creates a palette that contains a scrolling list of all the current text strings. You can sort the list by using the Sort button, and unsort the list by clicking on this button again. The default order of the items is the order in which they were created. You can pick a text entry from the list and the program will center on this text position. The map and bones will be displayed at this position if they are active.
This tool works in conjunction with the Validate tool on the main X-BUILD palette. Once validation is complete, the text markers created are linked to the error correction technique required to fix the errors (that is, bond errors are fixed by regularization). Any other text strings added by any other functionality are ignored by this tool. The current text error is fixed with this tool, and the text marker is changed to show that the error/warning has been fixed. Other validation errors may also be fixed, and these will also be updated to show the fix.
This brings up a scrolling dialog box of property information that can be loaded into the text editor. Currently these are:
You can pick an entry from this list, and the program will load in the relevant information. For example, if you load the water molecules, you can then use Goto next text and Goto previous text in the text editor to look at each water molecule in turn. The program does not write any of the property lists to the session file. When you exit the program, the list of user text labels is saved. You cannot add to or delete from the property list. You must use this option to load in the user text labels list of text items before you can add or delete text markers.
This puts away the Text palette.
This tool reads only the Ca atom coordinates from MSF information into X-AUTOFIT | CA Build. This allows homologous information to be read into X-AUTOFIT | CA Build to form the basis of the new structure while using the auto build algorithm to build new all-atom information only from the map. You might need to do this when a molecular replacement solution is to be generated. The new Ca trace is added to the current Ca trace information, so if you are loading an entirely new structure from an MSF, you should first delete all the old Ca trace information. The tool loads in the Ca coordinates for all visible and active molecules.
This selection generates a new skeletonization calculation centered on the current alpha carbon. You can select any alpha carbon atom as the active one to specify where the next bones box will appear. The origin of the bones box is shifted to this alpha carbon, and a new skeleton and map contours are displayed. Use this selection when your alpha carbon trace reaches the edge of the current bones box.
This selection accepts the position of the currently built alpha carbon and provides you with another alpha carbon to position. Next, Ca automatically executes a Guess next CA calculation and attempts to position the newly added alpha carbon. When you select Save changes, the currently active carbon is included in the saved set. If you cannot position the current alpha carbon, use Delete current CA to remove it before you save. You can also use the Undo last build selection to remove the current alpha carbon.
Repeatedly using Next CA does not have the same effect as using the Auto Extend tool in the X-POWERFIT palette, because auto-extension can build on information from previous Ca placements to improve the fit of the next Ca, while manual extension cannot.
This selection deletes the current alpha carbon and makes the previous alpha carbon currently active. If only two atoms are left in the segment, no more can be deleted.
This selection starts a new segment of alpha carbons at a new starting point on the skeleton. The Accept or Quit popup is displayed with selections that you can use for choosing the new point (see Pointer palette for a description of palette selections). Selecting Undo last build will delete the last new segment.
If you want to start at a point in the electron density map that is not currently skeletonized, you must recenter the skeleton using either the bones to pick a new point on the map, or the pointer to place the map center and then use X-AUTOFIT | Pointer | Goto pointer. If there is already at least one segment present, the new segment becomes active (default color red) and the previous segment becomes inactive (default color blue). You can return to the previous segment by selecting Current res | seg.
This selection deletes the currently active segment and makes the previously built segment the currently active segment. If only one segment has been built, it is deleted. Selecting Undo last build replaces the deleted segment.
This selection reverses the order (polarity) of the current segment. The current alpha carbon becomes the origin of the chain. The chain can be reversed at any time. This allows the current segment to be built in either direction. Selecting Undo last build will reverse the chain again.
Use this selection to change the alpha carbon and segment you currently have selected. The current alpha carbon is yellow and the rest of the segment is displayed in red. All other segments are displayed in blue. When you make this selection, the message line instructs you to select an alpha carbon. The nearest alpha carbon to your screen selection becomes the active carbon and the segment containing this carbon becomes the active segment.
If you pick a terminal alpha carbon, all selections on the palette and the dials remain active. If you pick an alpha carbon that is not a terminal alpha carbon, then the dials change so that the xyz position of the alpha carbon can be changed. The Ca plot changes to indicate the conformation of the alpha carbon you have selected.
Use this selection to join two segments of a Ca chain. The selection is grayed until at least two Ca traces have been generated for the bones skeleton. When the segments are joined, the single segment that is formed becomes the current segment.
This tool allows you to break up a segment. This is necessary if you have read your Ca atoms in from a file generated by O. O treats all fitted Ca atoms as a single segment regardless of the connectivity, but X-AUTOFIT treats the different fitted sections of Ca atoms as different segments. This incompatibility causes X-AUTOFIT to
join up all the fitted segments with very long bonds. The Unjoin 2 CA tool prompts you to pick a Ca-Ca bond. The bond nearest to the pick will be deleted. This splits the single segment into two segments; one becomes the active segment. If any sequences had been assigned, a sequence alignment is carried out for the two new segments, and any changes are updated.
This selection displays a pop-up to define the addition of a helical or beta strand Ca-trace whose length is defined by the number you type.
Select the secondary structure element to fit, and its length. The default is a 10-residue helix. The dial box will change to allow you to adjust the orientation and position of the element, the Accept/Pick dialog box will appear, and an idealized helix/strand object will appear at the current pointer position. You can use the dials to move the object until it is in the correct position in the density. The position can then be accepted from the Accept or Quit dialog box. No other tool is available while this positioning is in process. If you select Quit, no changes are made; if you select Accept, this idealized secondary structure element will become the current Ca-trace and the last Ca atom will become the current Ca atom. This trace can then be edited as any other trace of Ca atoms, or can be used as a template to aid in the building process, and then deleted at a later time with X-AUTOFIT | CA Build | Delete segment.
This tool allows the movement of the current segment as a rigid body. The dial box changes to allow the movement in x/y/z and rotation about the x/y/z screen axes. The Accept or Quit dialog box will appear. If you select Quit, no change is made to the coordinates. Otherwise the current segment is moved to the new position.
This tool carries out real space rigid body refinement of the current segment. This is most useful to improve the fit of a secondary structure element that was fitted with X-AUTOFIT | CA Build | Add helix/strand.
During refinement, a white line model of the segment is shown, and on completion, the Accept or Quit dialog box appears to allow you to either accept the new position or reject the changes.
This tool assesses the probability of the polarity being correct and reports that information in the text port. If you have defined any residues for any segments in the molecule, sequence alignments are marked in the molecular sequence table at the top of the molecule window. Blue arrows indicate forward alignment and red arrows indicate reverse alignment.
When you select this tool, X-AUTOFIT attempts to fit polyglycine to the trace in both directions, checking geometries. The following information is then reported in the text port:
The polarity of the active alpha-carbon trace can be reversed (Reverse chain option) so that building can be carried out at either end of the chain. You should evaluate the polarity of the alpha-carbon trace before you generate a peptide backbone.
This selection toggles a set of markers on and off. They highlight all the points that are 3.8 ± 0.3Å from the current alpha carbon. Use these as possible positions for placing the next alpha carbon.
This selection calls an assisted Ca building routine that selects the best conformation for the next alpha carbon. This selection is based on connected density, branch points near the test position, a reasonable Ca-Ca-Ca angle, and main chain/side chain bones.
Repeated picking of this tool will move the current Ca atom to a new guessed position. The Textport will print out the point number fitted and the rank order of likelihood. For example:
Number of OK points = 4
Point 1 main chain : impossible angle No branch
Point 2 main chain : OK angle near a branch
Point 3 main chain : impossible angle near a branch
Point 4 main chain : unlikely angle near a branch
Point 2 of 2 : order no. = 2
Note, as seen from this example, that "impossible" conformations (where the Ca trace would fold back on itself), are not counted in the number of valid points, and are not displayed by the Guess next CA tool. So in the above example, there are four theoretical points for the current Ca, only two are valid; the second is the currently shown on the display, and this is the most likely point.
Using the real space refinement procedure, this selection generates a polypeptide chain based on alpha-carbon coordinates that fits the electron density map. Color indicates the quality of the fit of the atoms. A green (by default) atom has been fitted well, a blue atom indicates that the atom has not been fitted because there was no density in the region. Other fit qualities scale between blue and green. If there is a sequence fitted to the Ca trace, then the all atom model for these residues will be build. If no unique sequence assignment has been made, then only a polyalanine model will be built.
If the sequence has been aligned, the sequence number for the built segment is taken from the sequential position of the Ca atoms in the sequence. If no sequence alignment has been set, the sequence is numbered beginning with 1.
The tool Fit segment by database allows the generation of all atom models based on database fragment building The fragment building algorithm uses the Ca distance matrix to determine five matches/fragment within the database of protein structures. For each five residue fragments, the five Ca-trace fragments are tested from the database to find the most likely conformation of backbone atoms. The backbone atoms are then merged together to form a contiguous polypeptide chain of polyalanine. If sequence information is known then the side chain atoms are added using grid real space torsion angle refinement into electron density.
Note that Fit seg by RSR is preferable to this method since it is statistically valid over a wide range of conformations and should always be used where the density is good enough to fit the side chain atoms. It is recommend that, although this type of building method is well known, you should use the tool Fit seg by CA correlation as this produces very precise results with very few errors.
If the sequence has been aligned, the sequence number for the built segment is taken from the sequential position of the Ca atoms in the sequence. If no sequence alignment has been set, the sequence is numbered beginning with 1.
This tool uses a superior algorithm to the Fit seg by database tool as a method of theoretical building of polyalanine polypeptide chains from Ca traces where there is little density. The tool uses a matrix of values that directly correlate values of Ca conformation found in the protein databank and the Ramachandran angles associated with these Ca conformations. The first use of this tool reads in the matrix of correlation values. Subsequent uses of the tool access the matrix from memory and are almost instantaneous. The algorithm determines the local Ca conformation, and then directly builds in polyalanine using the Ramachandran values within the correlation matrix. The algorithm reproduces polyalanine coordinates from Ca traces with RMSD values of 0.3A to 0.5A in test calculations. The very low residuals result because the entire information within the protein databank is used, but statistically removing the outlying results from the lower resolution crystal structures. Hence loops are generated correctly.
After fitting a polyalanine chain into the Ca trace, the tool fits the side chain atoms if the sequence information is known using real space torsion angle grid refinement.
If the sequence has been aligned, the sequence number for the built segment is taken from the sequential position of the Ca atoms in the sequence. If no sequence alignment has been set, the sequence is numbered beginning with 1.
It is not possible to fit main chain and side chain coordinates when the experimental information is very poor or non-existent. No map fitting occurs. The CA-build | Fit seg by D.E.E. tool fits main chain atoms using the Ca-Ramachandran correlation table and models the side chains by adjusting the conformation of the side chain chi angles and of multiple neighboring residues. The energy is computed for each possible conformation and the lowest conformation is retained at each residue. The conformation used in the analysis are rotamers taken from the current rotamer library. We recommend that you use the old library available on the Options... palette since it is extensive and contains values for chi 3 and chi 4 variations.
If the sequence has been aligned, the sequence number for the built segment is taken from the sequential position of the Ca atoms in the sequence. If no sequence alignment has been set, the sequence is numbered beginning with 1.
This tool deletes a currently selected fitted segment.
This selection will undo your last selection with the exception of Guess Next CA and Save changes.
This selection writes the current Ca trace to a session file, saving all the fitting done up to that time. This session file will be read in the next time X-POWERFIT is used, and therefore can be used as a backup file if necessary. Note that a save to the session file is made automatically on exit from X-AUTOFIT.
This application provides smart tools for Ca tracing based on secondary structure searching and assisted tracing tools. X-POWERFIT is based on the calculation and placement of vectors that represent the principal components of the secondary structural elements.
This tool is designed to determine the secondary structure from an electron density map. Before the tool is used, the bones must be active, and the start value for the bones set to a level that indicates useful information. The default value for the bones "start" is indicated in the table below for experimentally phased maps, but the use of the tool Bones | Map quality from bones may indicate more suitable values.
The tool can take several minutes to run. Generally, expect it to take approximately one minute for every 30 residues in the structure. Using highly over-connected maps (bones start value too small) significantly increases the calculation time! It should reliably find stretches of secondary structure, especially at lower resolutions (~3-4 Å).
This tool initializes the vectors, removing any previously calculated vectors. The tool is not available if a map or bones are not present.
Allows you to delete vectors placed using the Find sec. Struct. tool or placed manually or read from an external file. On selection of the tool, the application prompts you select a vector to delete. Pick the vector to be deleted. The tool continues to prompt for vectors to delete until there are none left, no vector was close to the screen position picked, or a palette tool was picked. Selecting the palette tool again aborts the command.
The Place-edit strand tool has three applications.
1. Reclassifying a helix as a strand.
2. Editing the position and length of a strand already present.
3. Adding a strand by picking two bones points.
When you select this tool the application prompts you to Pick bones or vector and the Accept or Quit dialog appears. While this Accept or Quit dialog is open, you can exit the tool only by picking Quit to reject any changes or Accept to accept the changes made.
If a helix vector (color 5) is picked, it is reclassified as a strand vector. If a strand or helix vector is selected, the dials change to allow the translation, rotation, and changing of the length of the vector.
If a bones point is selected, the application prompts you to pick a second bones point on the screen. The tool is aborted by any other pick. On picking a second bones point, a strand vector is placed so that the line joins the two bones points.
The new vector placed by this command is added to the list if Accept is clicked.
The Place-edit helix tool has three applications.
1. Reclassifying a strand as a helix.
2. Editing the position and length of a helix already present.
3. Adding a helix by picking two bones points.
On selecting this tool, the application prompts you to Pick bones or vector and then the Accept or Quit dialog appears. While this Accept or Quit dialog is open, you can exit the tool only by picking Quit to reject any changes or Accept to accept the changes made.
If a strand vector (color 5) is picked, it is reclassified as a helix vector. If a strand or helix vector is picked, the dials change to allow the translation, rotation, and changing of the length of the vector.
If a bones point is selected, the application prompts you to pick a second bones point on the screen. The tool is aborted by any other pick. On picking a second bones point a strand vector is placed so that the line joins the two bones points.
The new vector placed by this command is added to the list if Accept is clicked.
This tools allows you to save the current set of vectors to a file. The filename is secondary_structure.vec. This file is read using the tool Read vectors, described next. The vectors are stored in the following ASCII format, as 4x4 matrices.
Title card (format = a)
Number of vectors to follow (format = i6)
loop i = 1 ; number of vectors {
loop j = 1 ; 4 records {
matrix[i] [j , k = 1 ; 4 fields] (format=4f12.5)
endloop (j)
} endloop(i)
This tool allows you to read in a saved set of vectors from the file secondary_structure.vec. After reading the vectors, the display is changed to show the vectors read from the file.
This tool allows you to take the current Ca trace and search a set of pdb files for matching geometry. You must specify the number of Ca atoms in the trace, the cutoff for the RMSD between your trace and a candidate pdb file, and the directory path for the set of pdb files to be searched.
The Vector Search/Browse tool opens a dialog to allow you to search the protein databank by structure motif. The search uses vectors from the auto search of the secondary structure in X-POWERFIT or vectors placed manually.
If you have done a previous search, you are shown a list of previous hits and given the option to show the current hit. The hits are sorted by a weighted combination of rmsd and the number of motif equivalents in the scroll list.
You may start to browse the solutions before the run completes, since each time the dialog is opened, the current list of hits is read into the results box and sorted by quality of hit.
You can specify both the number elements to align and the allowed rmsd deviation over all the motif elements. The database filename can be changed if you want to search a private list. The PDB file path must be valid if you want to view the results.
$HYD_LIB/vector.base is the default list of vectors used during a search and contains all the proteins in the Protein Databank as of 1 November 1998.
You may recalculate the predefined vector list used in the alignment by using the motif searching program in generate mode. The program is found as $HYD_EXE/motif_align and should be run in the following way:
> $HYD_EXE/motif_align -generate -list (user-file- list) -database (user-vector-file)
The -generate option causes a database file to be created.
The -list option specifies that the next argument is a file that contains a list of protein filenames. Normally this is the current Protein Databank, which should contain the explicit path and filename of each protein on a separate line.
The -database option specifies that the next argument is the filename of the new database vector file. This cannot be overwritten by the program.
Generating a new database can take several hours.
If valid solutions have been read in using the Search | Browse DB tool, it is possible to view the next solution using the ...Next solution tool. This immediately reads in the next solution in the list and displays the results as a Ca trace.
If valid solutions have been read in using the Search | Browse DB tool, it is possible to view the previous solution using the ...Previous solution tool. This immediately reads in the previous solution in the list and displays the results as a Ca trace.
This tool converts the current solution displayed on the screen into an X-AUTOFIT Ca-trace segment(s). This Ca trace can then be modeled using the CA-build and X-POWERFIT tools.
Use the Current res. and seg. tool to change the alpha carbon and currently selected segment. The current alpha carbon is yellow, the rest of the segment is red, and all other segments are blue. When you make this selection, the message line instructs you to select an alpha carbon. The nearest alpha carbon to your screen selection becomes the active carbon, and the segment containing this carbon becomes the active segment. If you pick a terminal alpha carbon, all selections on the palette and the dials remain active. When you pick an alpha carbon that is not a terminal alpha carbon, the dials change so that the xyz position of the alpha carbon can be changed. The Ca plot changes to indicate the conformation of the alpha carbon you selected.
The tool Vector to CA-trace converts the reduced representation vector into a Ca-trace and hence increases the amount of information determined in the building process. The tool prompts you to pick a vector from the display. If no vector is picked or a palette tool is picked, then the tool does nothing. The tool uses a directed refinement algorithm to fit a "standard" helix or strand into the electron density. Since each vector is classified as either strand or helix (color 5 = helix, color 14 = strand), the tool can automatically determine the secondary structure type to fit. The length of the vector defines the length of the secondary structure element to fit, and hence the number of residues that will be fitted to the electron density.
Electron density must be present in the region of refinement for this command to produce a correct, refined solution. This command is not available if no map is present.
Cycles of gradient refinement are carried out along the principal components of the strand/helix. When fitting helices, the tool also carries out a directed helical refinement, in which the Ca trace is rotated and translated simultaneously so as to find Ca positions along the helix. As the orthogonal components of refinement gradient are separated for at least part of the refinement process, the radius of convergence is very high, on the order of 3 Å.
The tool returns a residual value to indicate whether the Ca trace fitted really does fit the electron density. The fit value is returned to the textport and shows the following information.
The refinement is very sensitive to the quality of fit and diverges rapidly when an incorrect structure is fitted to the map. Hence the residual is a very reliable indicator of fit. Alpha helices in proteins tend have a very restricted range of conformations, and therefore helices are placed with a great deal of precision by this command. Strand structure in proteins is very variable, and therefore this tool has less success in fitting this type of structural element. When fitting strands, make sure that the refined coordinates actually fit the map. In some cases it is more useful to place strands with the Auto extend CA command.
On picking a vector to place, a new Ca trace appears. After a short period of refinement, the Ca trace jumps to a new position and the residual is displayed in the textport. The new section of Ca trace becomes the current segment, and any previous Ca is colored so as to reflect the changes. If the new Ca trace is the first Ca trace, then all the masking of the palettes is changed to reflect the presence of the Ca trace atom, and the Ca plot appears if it is not already displayed. The new Ca-trace atoms can be edited, appended, and deleted by any of the commands on the CA Build palette. If a sequence table is open, then the new Ca atoms will have residue type "UNK".
This tool adds another Ca atom to the current segment if the current Ca atom is a terminal atom and only if the previous 4 Ca atoms lie in either a helix or strand structure. The tool places the new Ca atom in a helical conformation if the previous four atoms are in a helix and in a strand conformation if the previous four atoms are in a strand. Hence the tool is used to extend the secondary structure elements placed by the tool Vector -> CA trace but can be used on any general segment of structure if it is a recognized conformation (see the Ca plot). If the previous four atoms are not in a recognized conformation, then the tool stops and prints an error message to the textport.
The Auto extend CA tool is designed to add Ca atoms to the end of the current segment using continuous calls of the routine to add Ca atoms based on the bones and map. Hence this tool requires the presence of the map and bones before it can be used. The presence of vectors created with the Find sec. struct. tool provides the algorithm with additional information, which can improve the results (the vectors do not need to be displayed). The routine is very conservative and stops adding atoms if any of several conditions is not fulfilled.
The tool checks all the possible pathways for the next Ca, based on the bones, using two methods. For each pathway the Ca atom is refined into the density. The tool checks the Ca conformation for each pathway, whether the bones network is main or side chain in each direction, and for the presence of branch points at or near the test positions. The current secondary structure is also used to weight the pathways. The tool then checks the local and global build of the Ca trace by refining polyalanine into the Ca trace and checks the unrestrained geometries generated in the polyalanine chain. Since this building process is highly correlated, the local and global build are different. The routine stops if the build quality significantly falls in the local region or for the whole Ca trace, whenever a clash occurs, or if no pathway can be found in the map. If all conditions are satisfied, the new Ca atom is added and the process is repeated. The build can also backtrack to try alternative paths.
Ca building proceeds at about 2 residues/sec on an R4000 computer but does depend on the current size of the segment, since the global polyalanine test depends on the size of the segment. During building, feedback is provided on the quality of the build as a pie chart in the bottom left corner of the molecule view window. The filled portion of the pie chart represents the probability of the global fit of polyalanine in the best of the forwards and backwards directions. The pie chart remains displayed while building is occurring and is removed when the process ends.
Auto-building can be aborted by clicking the left mouse button at any time.
A large amount of output is written to the textport to allow analysis of the building progress, including the current quality of fit, whether the fit is improving or getting worse, and the reason for abortion of the building process. The coordinates of the automatically extended chain should be carefully reviewed.
The CA refinement tool allows a method of improving the fit of the Ca coordinates into a map based on refinement of the pseudobond lengths, angles, and torsions of the Ca trace. The refinement is highly restrained to retain reasonable Ca geometry. Bond length and bond angle restraints are included in the calculation. The tool also carries out rigid-body refinement of the segment. Significant improvements in the fit of the Ca trace to the electron density can occur.
The refinement is successful with large stretches of Ca trace, but due to the inherent correlation within a long segment of Ca atoms, the refinement can take tens of seconds to complete. Therefore some time can elapse between refinement cycles (and screen refreshes) as the algorithm removes this correlation. This tool is limited to 250 Ca atoms since correlation along the chain makes refinement very slow for large chains. Longer Ca chains must be cut with the CA build | Unjoin 2 CA tool.
This tool performs Ca tracing for lower resolution or poorly phased data. It is necessary that secondary structure vectors exist (Find sec.struct.) before this tool can be used. The tool then checks the helical vectors to determine the best quality helix within the map. A Ca-helix is placed using this vector, and the Ca trace is automatically extended from both ends of the helix. The tracing continues until an exit condition occurs. Exit conditions include No Path, Join point for CA trace, User defined abort or low quality fit.
The tool repeats this operation with each helix vector in the sorted order of quality until no more helix vectors are left or the map is traced. If there is still a map to trace, the same sorted order placement and extension occurs for the strands.
The build rate is approximately 1-2 residue/second and the number of residues fitted depends on the resolution and quality of phases.
It should be noted that the tracing method is a pathway analysis algorithm. This means that the method cannot jump a gap in the bones trace. The vector search algorithm works for a much greater range of bones start values, and generally a sigma value of 1.2 or 1.3 should be used with 2Fo-Fc and SigmaA weighted maps. The tracing algorithm, as it requires connected bones, should still be used on bones slightly over connected, for example, about 1.1 sigma for the start value.
It should also be noted that density modification sharpens a map, i.e., good bits get better, and bad bits get worse. Hence, DM maps are often more fragmented and with highly DM maps, a sigma level of 1.0 may be required if you want to trace the map in one go.
This tool performs Ca tracing for high resolution, well phased data. The tracing method is designed to determine a single solution from a simultaneous analysis of all the bones. This tends to be an all or nothing routine.
This tool uses an entirely different algorithm than previously available in QUANTA, although it is still a pathway analysis method. It is designed to be used on maps 2.0Å or better. There is no necessity for vector search, only that the bones be turned on and trimmed to the required molecular boundary. The routine is fast and generates a Ca trace that can be manipulated with all the tools in X-POWERFIT and X-AUTOFIT.
Turn on the bones, trim these and click this tool. Tracing occurs at about 50-100 residue/second.
The routine tends to fail to produce results rather than entirely wrong results. For data of the prerequisite quality it is sensible to use this tool first to check for reasonable results, and then use the Auto-trace Low tool if the data are not suitable. Of course the Auto Extend CA tool can be used on the results to continue tracing. It should be noted that at modest resolutions the routine can produce helices with not enough residues/turn. Be aware of this.
This tool carries out a multiple trace analysis of a protein to determine the optimal interpretation of a map. You must first calculate the secondary structure vectors using Find sec. struct. from the X-POWER-FIT palette before using this tool. The tool traces a map nine times and returns the best trace as the highest sum of atomic occurrence with variance 0.7Å.
This tool checks the current active segment of the Ca trace for knots. It indicates in the text port whether a knot was found. Click the tool to draw a graphic of the analysis progress and final knot path; click the tool again to close the graphic. Use the tool: X-Autofit | CA Build | Load CA Coordinates to import a Ca trace from an already built protein to check this. For example, the protein 1yve.pdb contains a knot.
The literature indicates that the process of creating folded protein from the DNA code means that any protein containing a deeply embedded knot is extremely unlikely. In the context of map interpretation, this tool is therefore used to identify bad connectivity.
This closes the X-POWERFIT palette.
This palette is only for use with the CA Build palette.
When you select this tool a dialog box opens to allow the selection of a sequence format and filename from which to read the sequence information. These formats are described in detail in the QUANTA Protein Design User Guide, Appendix F.
The Dialog box contains a file browser, a text field for a file name, and a multiple option list for different formats. The default format is PDB, and all the PDB files will be listed in the file browser.
1. From PDB: This option will read the sequence from the ATOM card information of a PDB file. The file browser will show all files with a .pdb extension.
2. From MSF: This option allows you to fill the sequence table from a MSF file. The file browser will show all the files with a .msf extension.
3. Free format: This is the original sequence reader and allows you to read the sequence from a file that has no particular formatting. The file should contain a single letter code of the sequence in either upper- or lower-case, with any number of sequence entries per line, up to 100. Spaces are read in as part of the sequence and can be used to delimit segment structure in the sequence because no alignment can be made across these spaces. Do not add spaces that are not segment delimiters. The file browser will show all files with the extensions .aa and .seq.
4. FastA: The first line of the file is the title and begins with a ">", and the rest of this record is the title. The sequence is read until a "*" or "eof" marker is encountered. Spaces and punctuation are ignored. The file browser shows all files with the extensions .aa and .seq.
5. GCG: The GCG file may contain an arbitrary number of lines of comment at the start of the file. These are followed by a blank line and then a title line. The sequence is written with 50 residues per line, each line beginning with the sequence number. These sequences are obtained from the GCG package. The file browser will show all the files with the extension .gcg.
6. NBRF: The first line contains a ">" in the 1st character position, and a ";" in the 4th character position, followed by the sequence ID. The second line is the title. Subsequent lines represent the sequence, terminated with a "*" character. Spaces are ignored. The file browser shows all the files with the extension .nbrf.
7. EMBL | Swissprot: The file begins with lines of comment which have two-letter keywords at the start of the line. The sequence is preceded by a line beginning with the keyword "SQ". The sequence is terminated by a line keyworded with "//". Spaces are ignored. The file browser shows all the files with the .embl extension.
8. Quanta sequence builder: The sequence builder option reads the sequence from the QUANTA sequence builder format file. The file browser will show all the files with the extension .qua.
If a sequence is successfully loaded into X-AUTOFIT, it will be displayed at the top of the main molecule window in lowercase letters. After loading the sequence table you can assign sequence information to Ca-trace atoms and any weighted fit will be displayed next to the sequence.
If a Ca trace is already present with sequence information (for example, after using X-AUTOFIT | CA Build | Load coordinates), then an alignment will automatically be carried out with the new sequence loaded. The alignment will be shown on the new sequence that is read in. If there are multiple identical domains in a protein (i.e., the ab+ab structure of the insulin dimer), then it is recommended that the sequence read in consist only of one dimer unit. Then use X-AUTOFIT | Sequence | Unique sequence to mask out already assigned sections during the sequence assignment.
This tool removes the displayed sequence and the alignment arrows, but has no effect on the Ca trace assignment.
This tool allows you to toggle on/off the display of the sequence.
Use this selection to change the alpha carbon and segment you currently have selected. The current alpha carbon is displayed in color 4 (default color yellow) and the rest of the segment is displayed in color 3 (default color red). All other segments are displayed in color 2 (default color blue). When you make this selection, the message line instructs you to select an alpha carbon. The nearest alpha carbon to your screen selection becomes the active carbon and the segment this carbon is in becomes the active segment.
If you pick a terminal alpha carbon, all selections on the palette and the dials remain active. If you pick an alpha carbon that is not a terminal alpha-carbon, then the dials change so that the xyz position of the alpha carbon can be changed. The Ca plot changes to indicate the conformation of the alpha carbon you have selected.
This selection is grayed until X-AUTOFIT assigns a unique sequence to a segment. When this happens, the selection is unmasked and highlighted. The sequence is written in upper-case letters in the sequence table and in not used in any further sequence alignment. If you toggle the selection, the sequence is returned to lower case and can be used in subsequent sequence alignments for other segments.
This tool returns all Ca assignments to unknown (UNK).
Use this selection if you decide at any point that the fit is wrong after a unique alignment is made by X-AUTOFIT. When you make the selection, X-AUTOFIT returns to the last fuzzy sequence that you defined. This selection is grayed until X-AUTOFIT assigns a unique sequence to a segment.
The Guess Sequence tool provides a starting point for assigning sequences for the current Ca segment. The quality of the results is very sensitive to the quality of the electron density, so this tool should only be used when the electron density is reasonable and at least 50% of the protein is traced.
The tool searches for matching patterns of aromatic residues in the density and the sequence (the aromatic residues in the sequence are colored white). A protein with no aromatic residues thus cannot have a sequence assigned with this tool.
The Guess sec. struct. tool will predict the secondary structure from the loaded sequence data. The tool will color the sequence table on screen using red for helices and blue for strands. This tool can be used to assist/verify the tracing of helices or strands in the structure.
This selection opens a palette listing the 20 common amino acids and the residue type "unknown". This palette is used to assign a specific residue type to the current Ca, which is color 4 (yellow)]. Selecting any residue from this palette will cause a sequence alignment to be carried out against the loaded sequence (if one is present), and the results of the alignment shown against the sequence.
This selection opens a palette listing the 10 fuzzy descriptions of density. This palette is used to assign a fuzzy residue type to the current Ca which is color 4 (yellow). Selecting any description from this palette will cause a sequence alignment to be carried out against the loaded sequence (if one is present), and the results of the alignment shown against the sequence.
This tool will undo the last assignment of sequence information.
This carries out a real space refinement on the specified residue. This is a particularly good method of placing waters back into density. If you have specified a RTD file (see Defining torsion angles for unknown residues), then this tool will actually do a torsion angle real space refinement of the picked residue; if the picked residue is an amino acid, the refinement will refine the side chain torsion and the N-Ca-C-O torsion. If a ribonucleotide is picked, the backbone torsions are refined and the single base torsion.
This tool provides a box of options from which you can select a Ponders & Richardson rotamer library conformation, or a trans conformation. (It is also possible to use the Sutcliff rotamer library or a new list of rotamers designed for the dead end elimination side chain fitting tool). The list of conformations is ordered by percentage of occurrence. You can also place as a trans conformation. For each conformation, the residue is drawn in white, with all the non-bond contacts from the residue. If you click on accept, you will get the new conformation, while quit will return the old conformation. This tool will also rebuild templated structures if incorrect or missing atoms are found.
This tool is not valid for DNA/RNA.
This will fit a side chain to electron density by searching the chi angles, and allowing some tweaking of the angles in the side chain. Bonds are not refined, and impropers remain correct. This may result in a slightly distorted residue, especially if there is not enough density for the residue. If there is no density the result will be undefined. If you pick a Ca atom then all atoms in the side chain are fitted, even the CB position will be moved to give a correct chiral center and approximately correct chiral volume. If you pick the CG atom of a lysine, then only chi 3 and chi 4 will be refined, there will be no change to the N, Ca, C, O, CB, CG atoms. If you pick an atom in the side chain beyond all rotatable chi angles you will get an error and the tool will abort. The routine also aborts for glycine and alanine residues.
Proline is treated slightly differently. The residue is fitted by rotating the imino ring about the N-Ca bond, and checking that there are no clashes with the oxygen atom on the main chain. The single allowed ring pucker is also refined between ±30° from planar.
If the residue has missing atoms, or extra undefined atoms, the residue will be completely rebuilt from the template. This is the best way to build incomplete residues, even from just a Ca atom.
This tool will fit the single base torsion in DNA/RNA.
This prompts you to select a peptide bond. The tool will refine the torsion Ca[i] - Ca[i+1] if you pick the C[i] - N[i+1] peptide bond. The omega angle is also refined to values in the range 168° to -168°. This option is not available for residues other than amino acids.
This option continuously refines all the side chain chi angles that follow a side chain atom that you are moving. For example, if you select this tool and move the Ca atom of a phenylalanine residue, the side chain will be continuously refined: the chi 1 and chi 2 angles change and the bond angles in the side chain are tweaked in response to the movements of the Ca atom. The moving side chain is drawn in white. The side chain will tend to stick in density until is suddenly fits into a new place. An Accept or Quit pop-up box prompts you to either accept or reject the changes you have made. You cannot pick any other palette option while in this mode of refinement. The same restrictions apply as with the Fit side chain by RSR tool for the last fixed atom, which is the one you are moving. Proline can also be fitted with this tool.
If you wish to move the N-Ca-C=O backbone group using this tool, then pick either the N, C, or O atom of the residue, and the backbone atoms will move as a rigid body. Pick the Ca atom to refine the whole side chain while retaining the position of the main chain N,C, and O atoms.
This tool will fit the single base torsion in DNA/RNA as the C1´ atom is moved.
This tool allows the peptide plane and omega to be changed with the dials. The peptide plane is rotated about the Ca[i] Ca[i+1] pseudo bond. Omega cannot be rotated by large values without creating bad geometry. Therefore, do not use this tool to create cis peptide bonds; instead, set (X-AUTOFIT | Options | Omega restraint) and regularize (X-AUTOFIT | Build atoms | Regularize) the cis restraints.
This tools allows you to edit a set of eight torsion angles along the nucleic acid chain. Two (deoxy)-ribonucleic acid monomer units are edited at a time with this tool, with a result that a total of eight torsion angles can be changed during one edit. These torsion angles are b-g-d-e-z-a-b-g for the two residues concerned. If the residues i and i+1 are edited, then the phospho-ester bond i-1/i remains connected and residue i+1 is always the moving residue with the results that the phospho-ester bond i+1/i+2 becomes detached. You must complete the edit with closure of the i+1/i+2 phospho-ester bond. It is possible to refine the length of this bond subsequently using the regularize tool.
The tool requires that a bond be picked to indicate the two residues to edit, this bond is always part of the i residue to edit, hence picking the bond P(i)-O5´(i) apparently edits the wrong set of bonds as this particular bond is not itself editable.
The torsion d is part of a five membered ring of the sugar, and hence determines in part the type of pucker of the sugar ring. This torsion is therefore highly restricted in the values allowed and large changes may produce inconsistent ring geometry. Changing the value of d does not move the base.
The values of the torsions edited are shown in the DNA plot window as moving circular markers, where residue "i" are green and the "i+1" residue torsions are blue. There are two moving symbols for the torsion angles b and g. All torsions are labelled on the model window using the two central atoms of the edited torsions.
This tool allows you to manually edit the side chain chi angles. You are prompted for a residue to edit. The current chi angles are written on the message line as you change them. The tool will abort if there are no chi angles in the residue, or if the backbone is incomplete for this residue. The dials are changed during this option; use the dials to change chi torsions. If you have an RTD file, a ligand can be edited or up to 100 rotatable bonds can be edited. If there are more than eight rotatable bonds then the top dial becomes a toggle for the current active dial set. The changed atoms in the side chain are drawn in white. The Accept or Quit pop-up box prompts you to either accept or reject your changes. You cannot use any other palette items when editing the side chain chi angles.
This allows you to move a single atom in x/y/z. The tool will prompt for an atom to move, which you pick from the main window. The dials are changed for this option to allow the movement of the atom. The atom is marked by a white cross. You are prompted to Accept pick box for this edit, and no other palette item can be picked during this edit.
If the bumps are turned on you will get all the bumps to all atoms.
This allows you to move a zone of residues in x/y/z and about x=0, y=0, and z=0. The tool prompts you to pick two residues, the first residue in the zone and the last residue in the zone. If the same atom is picked (and hence only one residue), then the atom picked becomes the center of rotation. If different atoms are picked (either in the same residue when editing a single residue, or in different residues), the initial center of rotation is the center of mass of the atoms picked. At any time during the move zone edit you can pick an atom and this becomes the center of rotation during subsequent editing of the zone. Note that if the atom picked as the center of rotation is translated, then the original position of the atom remains as the center of rotation, and not the translated coordinate.
The dials are changed for this option to allow the movement of the residues. The residues are shown in white during the edit. You get the Accept pick box. No other palette item can be picked during this edit. If bumps are turned on, you will get all bumps from the moving zone to the rest of the structure. Do not try to move a zone through the middle of the protein with bumps turned on as everything will grind to a halt!
This tool prompts you to select a terminal residue. You can use the dials to edit the last three phi and psi angles. The current phi psi values are shown on the Ramachandran plot. The moving molecule is shown in white, and bumps are displayed, if active.
This tool only edits the first two and last two residues within DNA/RNA due to the large number of torsions in the nucleic acid chain. The order of the torsions depends on whether a 5´ or 3´ end picked to be edited, as the moving residue is "i" for a 5´ edit and "i+1" for a 3´ edit.
When editing a 5´ end the changeable torsions are g-b-a-z-e-d-g, and b where applicable, for the residues "i+1" and "i" respectively where the residue "i" is the terminal residue. When editing a 3´ end the torsions b-g-d-e-z-a-b-g are editable for the residues "i" and "i+1" where the residue "i+1" is the terminal residue.
The values of the torsions edited are shown in the DNA plot window as moving circular markers, where residue "i" are drawn as green circles and the "i+1" residue torsions are drawn as blue circles. There are two moving symbols for the torsion angles b and g. All torsions are labelled on the model window using the 2 central atoms of the edited torsion.
The Flip torsion 180 degrees tool allows the flipping of recognized rotatable bonds in proteins, DNA/RNA and ligands. The routine will prompt for a bond from the currently displayed and active molecules. If a peptide bond is selected from a protein molecule then the peptide plane (N-C=0) is rotated 180 degrees about the Ca-Ca pseudo bond. This is commonly known as a pep-flip. If an amino acid or nucleic acid side chain bond is picked, and if this bond is rotatable, the atoms along the side chain will be rotated 180 degrees about the bond picked. This is useful when the validation procedure indicates that an HNQ error is present, and therefore the last chi angle of the respective residue should be rotated 180 degrees. It is also possible to rotate torsions within a ligand if this torsion is rotatable (as determined by the algorithm for calculating these), or the torsion is defined in the "lig.rot" file. A rotatable bond can be added or removed from a ligand using the tool X-AUTOFIT: X-BUILD | Build atom | add delete | define torsion by bond.
It is not possible to flip the phi, psi or omega torsion in proteins, or any backbone torsion in nucleic acids. This type of flip would result in connectivity problems within the polymer chain.
You can mutate any residue to any other, except for itself. The new residue is added regardless of any missing atoms in the residue to be changed. The tool prompts for a residue to change (pick any atom in the residue), then a palette containing the 20 amino acids appears, from which you pick the new residue. The new residue atoms are added so that the value of a chi angle that is equivalent in the residue before and after mutation is maintained. Any non-equivalent chi angle is set to the most likely rotamer.
The tool allows the mutation of a residue to one of the five allowed bases: cytosine, adenine, guanine, thymine, and uracil. The base torsion is set to the same value as found in the residue before mutations. No restriction is made on the Thymine/uracil pair for the DNA and RNA models.
Opens the Add/delete palette described in the next section.
This tool calls the QUANTA hydrogen bonding routine. The hydrogen bonds between the real, symmetry and NCS atoms are also calculated and added to the symmetry atom object. This is so that the hydrogen bonds are hidden when the symmetry atoms are hidden using the object management table. The tool does not calculate the hydrogen bonds between symmetry atoms and symmetry atoms. This is to reduce the amount of visual information on the molecular display so that you can concentrate on the interactions only between the real atoms and symmetry.
The tool acts as a toggle button. When toggled on, the hydrogen bonds are recalculated whenever there is a change in the coordinates. This can slow down the display of the screen after any edit. When this tool is toggled off, no hydrogen bonds are calculated or displayed. To reduce the time of calculation of the hydrogen bonds after editing a residue, you are recommended to reduce the Coordinate display radius on the Options... palette. A value of 20 Å is suggested.
This allows a residue to be dragged around using one atom in the side chain. When you pick this tool, you will be prompted for an atom. Pick an atom in the molecule. This residue is regularized to completion, after which you can move the picked atom. The dials change to allow the movement of the atoms in x/y/z directions. The moved residue is drawn as a new set of coordinates in colors ranging through green-yellow-orange-red, depending on the error in the geometry.
The Accept pick box appears so you can either accept or reject the changes. No other palette is available while this tool is active. A new atom in the moving residue can be selected at any time. Picking this atom will result in this atom being the moving atom.
This tool prompts for two residues that define the ends of the zone to be regularized, and then an atom to be the first moving atom. After making these three selections, the zone will be regularized to completion, which may involve waiting one or two seconds. The dials are changed so that the moving atom you picked can be moved in x/y/z directions. The third atom selected can then be moved and all the atoms are regularized about this moved atom. The moving atoms are drawn as a new set of coordinates in colors ranging through green-yellow-orange-red, depending on the error in the geometry. At any stage a new atom can be picked and the previous moving atom is freed. All fixed atoms previously defined remain fixed unless picked as a moving atom. Note that the first residue N atom is fixed, and the last residue C atom is fixed unless either is a terminal residue. You can move the atoms at any speed, but give the program a chance to catch up occasionally. This can be determined when the moving atoms become green again.
The changes can be accepted or rejected using the Accept or Quit dialog box. All other palette options are ignored while this tool is active. You can pick any atom in the moving zone at any time.
This allows you to regularize a zone of atoms to completion. The tool will prompt you to pick two residues that define the zone to be regularized, after which the atoms are regularized and updated. You will see the progress of the regularization as a set of coordinates that range in color through green-yellow-orange-red, depending on the quality of the geometry. The N atom of the first residue and the C atom of the last residue in the zone will be fixed. If the first or last residue in the range is a terminal residue, then it is left free to move.
Note that there are no explicit chiral centers set up for the sugar ring, which means that all forms of sugar pucker can be regularized, and that final coordinates will be that of the initial pucker. If you wish to change the pucker of the ring, use either:
Fixed atoms and non-bonding are supported for nucleic acids, while the options of dipeptide restraint, phi/psi restraint and disulfide restraints are not applicable and are ignored.
This will open a dialog offering the following four options:
Fixes all the Ca atoms in a protein.
Fixes all the main chain atoms in a protein
Allows you to add to the list of fixed atoms by picking atoms from the molecule. If, however, a fixed atom (marked by a white cross) is picked, this atom is removed from the fixed atom list. For example, it is possible to fix all the Ca atoms and then re-edit this list to free some of the Ca atoms.
Deletes the list of fixed atoms.
This displays a palette that allows you to color atoms by property. The Color atoms palette is described starting on page 179.
This prompts for a residue to edit, and then displays a palette containing information about that residue. The sequence ID and insertion code can be changed for the residue, while the occupancy and temperature factor for each atom of the residue can be changed in the dialog box. Two fields allow you to set all atomic values in the residue to the same value. If the toggle is set to TRUE, then on exit the application will set all atomic B-values and occupancies to the values specified in the fields next to the toggle, regardless of the atomic values. If the toggle is set to FALSE, then the atomic values of the two parameters are taken from the values in the atom list.
If you pick Cancel, any changes entered are ignored; if you pick OK, all the changes you entered are updated in the data. If you pick a residue with more than 15 atoms (such as a ligand), then there will also be Next and Prev boxes to allow you to scroll up and down the list of atoms.
This prompts you for a residue. All the nonbond contacts to this residue (not including 1-2, 1-3, and 1-4 bonding) are displayed as lines with distance markers. The markers do not go away until:
1. You pick another residue to show bumps.
2. You turn off the bumps from the Options palette
3. You move a zone, chi angles, terminal, atom, or atom + RSR.
This writes all changed coordinates to disk.
This changes all edits back to what they were at the last save. You can check the edit status of the atom using Color by progress (see page 179).
Puts away the Build atoms palette.
The Add/delete palette allows the addition and deletion of residue data from the data model. It also allows the reorganization of the peptide chain by applying the Create bond tool when a peptide or phospho ester bone is selected.
This breaks the bond selected. If a peptide bond or phospho-ester bond is picked, then the residues become (temporarily) termini, which you can edit using the X-AUTOFIT | Build atoms | Model first last 4 res tool. You can also insert residues using the X-AUTOFIT | build atoms | Add delete | Add res. to termini tool, or change the connectivity.
If a disulfide bond is picked, it is deleted.
If any other bond is picked, it is deleted temporarily.
This creates a bond between atoms. The tool prompts for two atoms to be picked which are then joined by a bond. If the bond is a peptide bond, you can use the Regularize option to join distant residues. You can only join an N-terminus to a C-terminus (or vice versa).
If a disulfide bond or any other bond is created, they are temporary bonds. There is no distance check for these newly created bonds.
The Create peptide link tool along with Delete peptide link allow you to change loop connectivity by cutting peptide bonds and then creating new ones (which may be very distant). You can then use the Regularize option to drag the residues to a new position.
This tool allows the definition or removal of a torsion angle in a residue that is not an amino acid or nucleic acid. The residue can then be rotated manually (Build atoms | Edit chi angles, Flip torsion 180 degrees), and also refined within any the real space torsion angle refinement algorithms. (Build atoms | Refine 1 residue, Structure | refine zone)
The tool first prompts you to pick an atom, which identifies the residue that should gain/lose a torsion definition. (If you pick an amino acid or nucleic acid, the routine aborts.) After the residue is specified, the tool then labels the residue with any currently defined torsions. These defined torsions are read from the file lig.rot. If this file is not present, it will automatically be generated using the rotatable bond analysis algorithm. If a bond is selected that is not currently defined as rotatable (and is a valid torsion: non-ring, non-terminating), then the application will add this to the list of rotatable bonds. If the bond selected is currently defined as rotatable, then this torsion is removed from the list.
The tool remains active until the tool bar is picked again.
On completion of the editing of the rotatable bonds in a residue, the file lig.rot is generated if not already present, or modified if already present. The definitions in this file will be used in any subsequent calculations. Note that the definitions for other residues are retained in the lig.rot file.
This tool allows you to assign a residue up to four alternate conformations. The second conformation is fitted to the second most distinct density pattern in the residue side chain, while the third and fourth conformations are slightly different from a trans conformation (to keep them distinct for addition).
Occupancies are reset so that the sum of occupancies for each atom is one, and B-values are reset to 20. The main chain and CB coordinates are identical - that is, they have no disorder if the clamp flag is set to true, and the main chain atoms will have slightly different positions if the clamp flag is false. For more about handling disorder, see the notes on clamping (B-conf clamped to A backbone).
This prompts for a residue to delete, and then removes that residue. If you select a disordered residue, only one of the disorder pair will be deleted, depending on the atom selected.
This prompts for the first and last residues, which define the range to be deleted. The residues within this range will be deleted from the data structure. You cannot delete an entire molecule with this tool.
The program prompts you to pick a terminal residue. If you do not pick a terminal residue, this tool aborts. The program will then display a pop-up palette of amino acids. When you pick a residue from this list, it is added to the terminus by real space refinement. The algorithm used to fit the terminal residue will go back to the previous residue and fit the phi and psi angles from this residue, and also the phi/psi (depending on whether an N or C terminal was added) of the new residue. Therefore you must have electron density contoured about the old terminal residue. Then, the side chain of the new residue is fitted. The addition of residues by this method is very accurate for well-defined density, there is normally no limit to the number of residues that can be added in a chain. You should not use this tool to carry out de novo density fitting; the Ca-trace method is far more powerful in cases where density is ambiguous.
The Add Residue tool will allow the addition of a nucleic acid to the terminus of a DNA/RNA structure. The tool will first prompt for the selection of a terminus to which to add a residue, and if a nucleic acid terminal residue is picked, a palette appears so you can select one of adenine, cytosine, guanine, thymine, or uracil. If this palette is not picked, the tool aborts. The residue picked from this list is then added to the terminus of the polynucleotide in the conformation defined on the Options dialog box (beta/alpha/Z1/Z2). No restriction is made to the addition of uracil and thymine to DNA/RNA. If DNA is being extended, a deoxyribose sugar is added, otherwise a ribose sugar is added. The residue is not fitted to the experimental data, but set to a predefined conformation set in the Options dialog.
This places a water at the current pointer position. Then you can refine with the rigid body refine routine. If there are already waters in your data, the new water is placed at the end of the current list of waters in the coordinates, and is given the same segment ID and a residue number 1 greater than the previous water in the list. If you have no waters in your data, then a new segment, W, is created, and the new water is given the residue number 1.
This opens a dialog box with a list of cations and anions, from which you can select one to place at the current pointer position. Once added, the new atom(s) can be refined with the tool X-AUTOFIT | Build atoms | Refine 1 residue. If there are other metals/ligands in your coordinates, each new ligand/metal is added at the end of the coordinate list and given the same segment name and a residue number 1 greater than the previous metal/ligand in the list. If this is the first ligand in your coordinates, the new one is added to the end of your data, and a new segment is created with the name Z.
X-AUTOFIT supports various standards for C-terminal oxygen atom naming. This tool allows you to change the C-terminal COO group from/to any of the following conventions: O only, O/OXT, OCT1/OCT2, OT1/OT2, O/OE, O/OT. On picking the tool, the application will prompt for a terminal residue. If an N-terminal residue is picked, then, for polar hydrogen and all-hydrogen modes, three hydrogen atoms will be added. For a C-terminal residue, a dialog box will open that allows selection of one of the terminating types.
The tool to repatch a terminal in DNA will change the 3´ end of DNA/RNA so that an H3T will be added to all hydrogen or polar hydrogen DNA/RNA structures. If a 5´ end of a DNA/RNA fragment is selected to repatch, a dialog box with these options opens:
1. No phosphate: If present, the phosphate group is removed from the 5´ end of the polynucleotide chain.
2. Phosphate - O5T: If not already present, a phosphate group is added to the selected 5´ end, and no terminating oxygen (or hydrogen where relevant) is added. This will leave an unsatisfied phosphate group.
3. Phosphate + O5T: If not already present, a phosphate group is added to the selected 5´ end, and an O5T oxygen is added to the phosphate to complete the terminating phosphate. If hydrogen modes of All Hydrogen or Polar Hydrogen are used, an H5PT atom is also added.
This tool is used to show B-values or U-matrix values for an atom, a residue, or for all the displayed atoms. The display consists of three orthogonal circles/ellipses that define a one sigma deviation about the centre of an atom for isotropic/anisotropic motion. For the anisotropic display the principle axes of the ellipse are along the principle directions of motion of the atom as defined by the U-matrix.
A dialog box gives you the choice of B-values or U-matrix display, and whether the display shows an atom, a residue or all displayed atoms.
The B-values are taken from the atom B-values stored in the MSF file while U-matrix values are only read from a PDB file of the same name as that shown in the molecular table MSF file. If there is no PDB file of the same name as the edited molecule, then no display is added.
A scale value scales the spheres and ellipses drawn. The default value is 1.
This allows the simple consecutive renumbering of sequence IDs for each segment after insertions and deletions. You can interactively specify a range of residues to renumber or specify the starting sequence ID.
Puts away the Add/delete palette.
Colors the atoms by element type. The default scheme for view coordinates is:
Colors the atoms by fit to the map. The color range is a scale of:
The green atoms fit well and the red atoms fit badly. The blue atoms are those outside the currently loaded map extent.
Colors the atoms by the value stored in the B-values, where an absolute scale of Å2 is used. For example:
Colors the atoms by the occupancy value, where the occupancy data is normalized to lie between 0 and 1, and the following colors are used for 4 different relative ranges:
Colors the B conformer of an alternative conformation pair a single color (Color 14, pink).
Puts away the Color atoms palette.
On picking the tool for fragment fitting, all currently open X-AUTOFIT's/X-BUILD palettes will be hidden and the Fragment fitting palette appears. Note that the molecule that is edited in the fragment fitting application is the first visible and active molecule.
The Fragment fitting palette is described in Creating a Fragment Database.
On completion of the search for fragments, the previously open X-AUTOFIT | X-BUILD palettes are re-displayed. If any changes have been made to the structure using the fragment fitting application, then the molecule changed will be marked as edited, and you will need to save it when you exit from the X-AUTOFIT | X-BUILD application. Changes made in the fragment fitting can be undone using Undo last fit on either the Build atoms palette or Structure palette.
This allows the rigid body refinement (in real space) of entire sections of structure. If a complete domain is selected then the whole domain will be refined. The radius of convergence is not as large as in reciprocal space, but it may be able to improve some fitted regions. The algorithm uses gradient refinement on the six degrees of freedom defined by the rotations and translations of the zone to be refined. Occupancy information is used as in all refinement techniques. The refinement resolution factor defined on the Options palette is described on page 211. The tool prompts for the first and last residues in the refinement zone to be refined and, on completion of the refinement, asks whether to accept changes or quit.
The refinement algorithm uses torsion angle and rigid body refinement on a residue basis for each residue in the refinement zone, with cycles of regularization including non-bonding. The radius of convergence of this type of refinement has been found to be very high (on the order of 1.5/2.0 Å), and allows rapid refinement of regions of the protein. Although the algorithm can be used for refinement of an entire protein, you should not do the final refinement of proteins with this protocol.
The refinement is carried out in real space to the current map. The map must cover the entire region of refinement, since atoms with no experimental data contribution will move only as a function of geometrical restraints to other atoms. The algorithm will move atoms about torsion angles. The geometric restraints always include bonds, angles, impropers, and non-bond overlaps. If the phi psi restraints are active then these are used also. The non-bonds will only be defined for atoms displayed, so if there are symmetry overlaps, then the symmetry atoms must be visible for these contacts to be used in the refinement. (See the options palette, and the tool to change the symmetry radius). The refinement factor on the Options palette can be used where the density is poor due to lack of high resolution data, and this protocol has been shown to be useful on data of up to 4.0 Å. Occupancy information is used as in all refinement techniques. The refinement resolution factor defined on the Options palette is described on page 211. The tool prompts for the first and last residues in the refinement zone to be refined and, on completion of the refinement, asks whether to accept changes or quit.
The loop fit and terminal fit algorithms both use a Monte Carlo protocol to determine loop conformations that match electron density. The tool prompts for a start and end point for the search; all the residues in the selected zone must be covered by the electron density. The density for all atoms not part of the selected zone is masked to act as a precalculated non-bond list. The algorithm then generates random conformations defined by the phi and psi angles in the selected zone, and, if running a loop fit, checks that the end-to-end distance of this conformation will approximately fit in this region, and then carries out a density fit.
The conformations are generated at a rate of approximately 2000 per second, and the best ten fits are retained. Initially the search is slow, as the display of the first few new hits will be relatively slow compared to the search speed. Because of this, these algorithms accelerate over the first few seconds. This is particularly apparent with the terminal fitting. The ten best fits are displayed during the search and colored by fit to density. Green is a good fit; red is a bad fit. The calculation continues until you interrupt it by clicking in any QUANTA window with the left mouse button.
After interrupting the search, if there are some solutions to the search, the tools on the Fitting palette will become active, and all other X-AUTOFIT tools will be inactive. The solutions found to this point are sorted by fit to density, so the best solution found so far (by density fitting), becomes the active loop.
The continue search tool allows the search to be resumed, with the solutions found up to this point still active.
Fitting | Show next conformation Draws the next best conformation in the list of solutions, as defined by fit to density. If the current conformation is the last conformation in the list, then show next conformation shows the first conformation.
Fitting | Show previous conformation Draws the previous best conformation in the list of solutions, as defined by fit to density. If the current conformation is the first one in the list, then show previous conformation will show the last conformation in the list.
Fitting | Show all conformations Displays all the conformations found so far. This allows a check to see if there is a cluster of possible solutions.
Fitting | Accept If the Accept tool is selected, the current active loop becomes the actual coordinates for the main chain atoms, and the side chain atoms are added by real space refinement from the Ca positions found by the search.
Fitting | Quit aborts the loop fit option and does nothing.
The loop search will always fit a poly-alanine backbone trace to the electron density regardless of the sequence, but, for glycine, the CB atom will have zero occupancy.
The loop searching will only allow searching for complete residues, so if the loop has not been built, build a random conformation to complete the loop (see XFIT | Build atoms | add-delete | add-residue-at-termini on page 176) and then do loop fitting.
This tool allows a refinement protocol to be used on a range of residues. This tool is most useful for automatically refining the position of all the waters in a macromolecular structure, while X-AUTOFIT checks the changes made to each water by refinement. If any changes occur that are outside user-defined limits, the Do all tool stops and centers on this residue so that this water can be edited.
The Do all tool opens the Do all... dialog box.
Do all | Change all This allows the selection of the residue type or zone of residues to be refined. If Change all Water is selected, X-AUTOFIT checks all MSF files currently open; if any residue is a water molecule, then this is refined. If the Protein option is selected, the range of residues is defined by the amino acids in the first displayed and active molecule. The Start from Sequence ID Segment ID option is set at the current residue by any of the following:
The Select zone by atom name tool allows a specific range of residues to be refined. Two pop-up boxes appear. The first asks for the segment name, atom name, and sequence ID for the first residue in the range. The second pop-up prompts for the last atom specification in the range. If any one of the segment name, atom name, or sequence ID is not found in the MSF, then Do all aborts.
Therefore, your first use of Do all would normally be to apply one of its first two options. When this fails because the residue has become badly built by refinement, the current residue will be set to the next residue after this. The next use of Do all requires only that the Start from Sequence ID Segment ID option be selected. Note that if a badly refined residue (for example, if a water had no density) is deleted, then the residue that follows the deleted residue becomes the current residue.
Do all | By Protocol... The By protocol parameter allows the use of:
Some combinations of Change all and By protocol are not valid (for example, sidechain fitting of waters). For these conditions, Do all aborts.
You can also abort the Do all tool by clicking the left mouse button in any QUANTA window.
For each residue of the required zone, X-AUTOFIT will move the display to the residue (or water) that is to be refined, refine this residue (or water) by the protocol defined, and then check the abort conditions. If no abort condition is registered, X-AUTOFIT will move to the next residue and repeat the operation. If an abort condition occurs, then the Do all tool will write a warning to the text port and return control to you.
The Refine all water tool automatically places all the water molecules into available electron density for the first visible and active molecule. The tool carries out ten cycles of unrestrained real-space refinement of all the water molecules, with nonbond energy refinement to all other atoms that are visible and to the symmetry-generated atoms. This tool supersedes the Do all... | water fit since it simultaneously fits all the waters, checks water error correlated to other water positions, and is much quicker.
The tool returns 3D text notes on each water molecule where a problem is encountered. Several errors can occur:
Clash distance (non-bond clash)- Any water molecule under refinement will stop shifting along a gradient if a nonbond clash occurs with any other atom in a visible molecule or its symmetry-generated atoms. The water will be labelled with a text string to indicate that a nonbond clash has occurred and hence refinement has not converged. No account is taken of partial occupancy waters since water pairs (or higher orders) with 0.5 occupancy often converge to the same point. The tool will therefore warn of nonbond clashes even for partial occupancy waters so that you can handle these water molecules separately.
Move distance (Shifts too large) - Any water molecule that moves more than 0.2 Å during the final refinement cycle will be marked as having shifts too large. This generally occurs for water molecules that begin the cycles of refinement a long way from any minimum position. It highlights water molecules that may not have been fully refined.
Low density - A water molecule is marked if it remains in poor density.
Ref. steps - Any water molecule that has not converged during cycle 10 because the number of internal steps is exceeded will have this error label. This occurs when the gradient of the map is very small or complex, and hence convergence is not complete
Repeatedly using this tool will progressively remove the shifts too large and refinement stepserrors without any change to the converged waters or the waters with Non-bond clash. The user should check errors on the un-converged atoms.
The tool will indicate the number of waters to refine, and, if none are found, a warning is printed. The most likely occurrence of this warning is that the first active and visible molecule contains no waters. Non-bond interactions are calculated to all active molecules regardless of their visibility.
A new tool ...Delete bad water is available. This tool can only be used after the Refine all water tool and acts on the error messages generated by that tool. To delete less waters, use less stringent restraints in Refine all water.
This tool can ONLY be used after Refine all water and acts on the error messages generated by this tool. The Delete bad water tool deletes all waters with error messages generated by the water refinement. To delete fewer waters, use less stringent restraints in Refine all water.
It is possible to fit the side chain coordinates of a residue using modeling techniques where the experimental information is very poor or non-existent. The Fit by D.E.E. tool will prompt for start and finish residues and carry out the placement of the side chain atoms by adjusting the conformation of the side chain chi angles of multiple neighboring residues. Note that the neighboring residues are also changed while calculating the zone of residues.
The energy is computed for each possible conformation of a residues and its closest neighbors and the lowest energy conformation is retained for each residue during the search process.
The Undo last fit tool re-reads the session file from the last save of changes. This has exactly the same action as XFIT | Build atoms | Undo last, as they both act on the same set of tools and changes. Any changes made since the last save will be undone and the previous coordinates and residues restored. This can be used when a modeling session has gone wrong, and all changes need to be deleted. You can check the changes that will be restored using the XFIT | Build atoms_color by progress tool.
This tool regularises a range of residues based on a single residue selection picked by the user. The default for the residue range is +/- 1 residue. The default values can be changed with the tool Regularise param. This tool is suitable for use when active residue is turned on.
This tool regularises a volume of residues based on a single atom selection picked by the user. The default for the volume is 6 Å. The default values can be changed with the tool Regularise param. This tool is suitable for use when active residue is turned on.
This tool can be used to change the values for the residue range and volume used by the Regularise range and Regularise volume commands.
This tool carries out a real space torsion angle refinement for all residues (including ligands, but not water) within a volume about a selected atom. The tool requests a single atom pick, or uses the last picked atom when using active residue mode. The radius of the refined volume is set using the tool Regularise parameter on the same palette, and the default is 6Å.
This tool automatically runs through the entire fitted residues and fits them using a mixed grid and gradient protocol. It take three residues, fits the side chain of the center residue by Grid refinement. Refine Zone is then used on the main chain atoms only of all three residues, followed by side chain fitting of the two edge residues by Grid refinement. This is repeated for five cycles. The final stage is a round of regularization. This tool can work through gaps/missing regions of the structure.
This tool provides a simple interface to change the value of the temperature factor or occupancy of the first current active and visible molecule. The tool allows the setting of all atoms--just the main chain atoms or just the side chain atoms--to a user defined value.
This tool allows you to automatically redefine the sequence of the first current visible and active molecule. There are four options:
Puts away the Structure palette.
This palette is used for the advanced analysis of proteins (in particular) and other macromolecules. The tools available in this palette are used to generate tables containing information on atoms, residues, and undefined data. The data tables can be operated on by a number of functions, and plotted in a number of styles. The graphs and tables can be picked to centre the molecular view, while the graphs can be annotated and plotted to a postscript format file. Hence it is possible to use the table and graph information to zoom in on possible problems within a crystal structure solution, and use this for advanced validation.
For more on table usage, see the X-AUTOFIT:X-BUILD Tools chapter.
The Read file tool opens a directory browser dialog with two sets of options.
1. The Text handle option controls how the text information read from the file is placed/not-placed into the new General table.
2. The data placement option controls where the data will be put into an already existing General table.
This tool will read the currently displayed and active molecules into the atom table generating the columns: atom name / residue name / Sequence number/ x / y / z / occupancy / B-value.
Atom and residue ID columns are also generated but hidden. This is used for table and plot picking. The current contents of the Atom table is always overwritten by this action, and any reference by picking graphs or the residue table may be incorrect if the atom table is updated with a different molecule.
This will delete the currently selected columns of data. If no columns are selected, nothing is done.
This will delete the currently selected rows of data. If no rows of data are selected, nothing is done.
If rows of data are deleted from the residue table or atom table, data inconsistency can occur. This is a minor problem since, because the remaining rows of data will be correctly marked, there will be no referencing errors between the tables and molecule view.
This will open a dialog box to allow the deletion of a table. This is necessary when the displayed and active molecules have been changed, or when 1 or more residues have been deleted from a molecule. In both cases, a serious data inconsistency can occur.
This tool opens a dialog box to allow data selection in any of the tools for generating the tables: Read molecule, Column function, Protein Property, and Differences. The toggle boxes allow you to select protein, nucleic acids, water and ligands where the ligand option is defined as any residue type that is not an amino acid, nucleotide, or water. By default, data is generated only for amino acids and nucleic acids.
All currently open tables are deleted if the atom selection is changed since inconsistent data would be produced.
This tool will open a dialog box to select a function to apply to the current selected column(s). If no tables are open then the tool will abort. If no columns of data are selected then the dialog box contains a table and column selection boxes. All data in the column selected is operated on regardless of the activity of the molecules.
The dialog consists of three scrolling lists of functions:
Sin, Cos, Tan, ArcSin, ArcCos, ArcTan, SinH, Cosh, TanH :Trig functions, probably not very useful.
Square, Root : Takes the square and root of the data respectively
Abs, -Abs : Takes the absolute value of the data, + negative of.
Negate : Calculates "zero - datum"
Ln, Log : Natural log and Log(10) of data
Exp : E^datum
Prob : Determines distribution of data by finite size bins.
Copy : Makes a data copy.
NoDat->0: Changes all occurences of NoData to a zero.
0->NoDat : Changes all occurences of zero to a "NoData" flag.
Zero-Tor, Pos.-Tor, Neg.Tor : These functions apply to torsion data which are calculated to lie between -180 to 180 degrees. The zero function changes the data to -180 to 180, the Pos. function changes data to the range 0 to 360 degrees and the Neg. function changes the data to lie between -360 and 0 degrees.
This opens a dialog that allows the four basic operators of (+/-/x//) to be applied between two table columns. Both columns of data must be in the same table. The result is placed into the same table as the original data.
This allows the generation of data as derived from the molecule. Most of the functions apply to amino acids, though some can be applied to any other type of residue. Two scrolling list of functions are opened from which a function can be chosen. The last function used will already be entered into the text box.
This allows the calculation of derived values from the current visible and active molecules.
Mean bond length to each atom : atom information
Mean bond angle to each atom : atom information
User bond : atom, residue, or Undefined data produced
User angle : atom, residue, or Undefined data produced
User torsion : atom, residue, or Undefined data produced
Omega : residue information
Phi : residue information
Psi : residue information
Chi 1/2/3/4 : residue information
CA-CA distance : residue information
CA-CA-CA angle : residue information
CA-CA-CA-CA torsion : residue information
These functions return the difference between a value calculated from the molecule, and a standard value.
Bond Error to each atom : atom information
Angle Error to each atom : atom information
User bond error : atom, residue, or Undefined data produced
User angle error : atom, residue, or Undefined data produced
Omega error : residue information
Rama.Energy : Residue information - energy from a pre-computed energy surface for Ramachandran angles of (ala-ala-ala)
Rama.OUB.Dist : Residue information - Distance from the hard sphere 90% surface if not-allowed, or zero if inside the 90% hard sphere surface.
Non-bond clash : Atom information - Sum over all non-bonds to each atom of the distance to close compared to allowed value. Zero if OK.
Chi 1/2/3/4 Error : Residue information - Torsion angle difference from value determined and the nearest rotamer library value for that residue
CA-CA Error : Residue information
CA Improper Error : Residue information
Side Chain Improper error : Residue information - sum over all of chiral and prochiral errors in side chain. No-data if none.
Nomenclature Error : residue information - Torsion value if not valid, Zero if valid, No-data if no data
HNQ Hbond Error : residue information - Numerical difference in Hbonds between alternate conformations if wrong, zero if OK, No Data if not valid residue type.
HNQ Bvalue Error : residue information - Numerical difference in B-value if incorrect, zero if OK, NoData if residue type is wrong.
User defined properties in the property list.
The user properties are found in the list of properties and property errors. These allow the user to return data that is bond, angle and torsion based and defined by an atom name/sequence offset list. This is input from a dialog box that will appear. For example consider the calculation of the chi 1 torsion angles as shown in the following dialog box.
The atoms offsets are 0,0,0,0 as all atoms come from the same residue. The atom names are n, ca, ?b*, ?g*. The ? specifier means that any single character can occur at this position. The * specifier means that any number of characters can occur at the end of the string.
For the calculation of the omega torsion, the atom offsets are 0,0,1,1 and the atom names are: ca c n ca.
The two option lists Average over and For... determine how the data is averaged for placement into the tables.
This defines whether the data is to be returned as atom/residue or as is data.
This specifies how the data is placed into the data table where there is more than one value per data table row.
For example, consider the user bond [c* *], i.e. all bonds to carbon atoms. This will return multiple values to each carbon in the structure. If one is selected, the last value found for an atom/residue is taken as the returned data, and placed into the respective table. This is OK where the data is unique for an atom/residue. The each option will average all the values found to an atom/residue, and put the mean value into the table. The latter option is more sensible for the [c* *] example.
This tool opens a dialog box that allows the determination of differences between two molecules or two segments in the same molecule (for example NCS with restraints).
The first active and visible molecule is used as the reference molecule for all calculations. The Match molecule is selected from the top scrolling list of molecule names. If the same molecule name is selected as the reference molecule, segment comparisons are made and the Seg. align input strings are relevant. If the molecule selected is different from the reference molecule, differences are calculated between the molecules, and the Seg. align input boxes are ignored.
The XYZ option list is relevant for XYZ differences in position calculations only. The options allow deviation plots between the molecules/segments without a LSQ alignment, with LSQ alignment based on all matched atoms, and LSQ alignment based on Ca atoms.
The Difference type scroll box allows the selection of the type of difference calculation:
The Seg.align entry fields allows the definition of the segment names for the alignment of segments where the match molecule is the same as the reference molecule.
XYZ and B value data are returned to the atom table and the torsion values are returned to the residue table. The table entries filled are defined as the matched atoms in the reference molecule, for the segment deviations, only the first segment information is filled.
Opens a dialog box to allow multiple graphs lines to be generated from a set of table columns. If the table columns are selected, then the dialog will be filled in with the details of these columns; this is by far the easiest method of setting the plotting dialog. If no data columns are selected 3 default plot information dialogs are generated, the second and third have a zero Y data value to indicate that nothing is to be plotted.
Only one X ordinate is allowed; the table entry for this is defined by the first selected column, or the atom table if there is no selected column data. The default X data column is "0" to indicate that a numerical count is to be used for the X data.
The graph will be plotted if OK is picked -- nothing is done if Cancel is picked. Note that only one graph window is produced, and previous graphs are overwritten.
This opens a dialog box to allow the postscript file output to be changed. This effects the plot generated directly from the table and graphs plots, and also for the current session any plot generated from any Graph plot (not molecular view).
Step [0.5] - step size for any manipulation (inches)
X/Y [=] - make the size of plot so X = Y
X/Y [-] - Decrease the X size of the plot
X/Y [+] - Increase the Y size of the plot
[U] - Move plot up
[>] - Make plot smaller
[L] - Move plot left
[R] - Move plot right
[<] - Make plot bigger
[D] - Move plot down
This brings up a dialog to allow the annotation of an X-BUILD graph plot.
This palette is designed to allow you to create a custom palette of tools using any of the tools from the rest of X-BUILD, X-AUTOFIT and X-POWERFIT. It is also possible to set up macro tools that carry out more than on operation when picked.
When active, this allows the user to select any tool off the palettes of X-AUTOFIT/X-POWERFIT/X-BUILD (licensing dependent), and these tools are added to this palette.
When picked, the user is prompted to pick tools from any of the palettes. None of the tools (except those that open other palettes) perform their normal action, but rather place the tool picked as the next tool on the User defined palette. If a tool is picked for a second time, or picked on the User defined palette then this tool is deleted from the user defined palette. This may also used to delete a macro from the User defined palette.
When tool picking is active the ...add menu space and ...Clear all tools become un-masked.
The define new tools mode is exited by picking Define new tools again.
This tool is used for generating macros. Macros are tools that carry out more than one function. When active, and the user picks a tool, the program first prompts for a macro group name (via a pop up dialog), and then the tool picked is added to the macro group. The user continues to add tools and finishes the macro group by picking the Define-edit group tool again. The macro group folds up and is shown as a <>group-name
For example - pick a residue, fit side chain to density and regularize.
Pick > Place using coord: The application prompts for a macro-group name [Pick atom & fit/reg]
<> Pick atom & fit/reg : appears on the user defined palette
-> Place using coord: appears also
-> Active residue on: appears on palette
-> Fit side chain by RSR: appears on palette
-> Regularize: appears on the palette
-> Active residue off: appears on the palette
The palette folds to show only the tool <> Pick atom & fit/reg
If this tool is subsequently picked then all the operations in the macro are carried out sequentially. In this case the program prompts for an atom pick, fits the side chain to density, then regularizes the residue.
Do not provide a blank macro name (no string).
Do not provide a macro name already used.
In both cases the first occurrence of the name will be the tool used.
Adds a menu space after the current tool entry during define new tool entry
Clears all the tools from the palette. If immediately pressed again, the clear is un-done.
The Protein validate tool provides some simple validation procedures to check that the current active visible molecule conforms to the requirements of the protein data bank, as well as warning of deviations from expectation.
If a toggle box is checked, the validation indicated will be carried out on the first current active and visible molecule. The validation will generate text marks at each error residue which can be automatically fixed with the 3Dtext tool fix validate error.
It is possible to validate a structure at three levels of stringency. There is a options button at the bottom of the validate dialog to choose the required preference for deviation allowance.
At the bottom of the dialog is a check box to determine whether a log file of errors is written. The errors are collated as a function of each residue, and a list of each residue is made, and all errors associated with a residue are listed for each residue entry. Hence an error can occur in more than one residue -- for instance, for a non-bond error.
This tool can be used to find all the places in a map where atoms of the first displayed and active molecule overlap with negative density in the electron density map. Hence this tool is a validation method. You define which map to use with the tool Set bones | RSR map.The usual map to use would be difference density.
On selecting this tool a dialog box appears that prompts you for a threshold value to use in searching the electron density.
The threshold value is defined in map sigma, and the default value is -3.0. If you select Cancel, no action is taken. If you select OK, the application will read in the entire map and search for all peaks in the map that have a minimum below the threshold value. The peaks are clustered to remove errors closer than 1.0Å apart. The application will search all the current open MSF files for the closest coordinate to each peak and create a text label based on the peak depth and the nearest atom to this peak:
Neg P -> B Leu 11 CD1 : -3.14
The text labels can then be used in the 3D text editor X-AUTOFIT: X-Ligand | Text.... One use for this validation tool would be in the placement of water molecules into electron density. After placement of water, some of the water sites can develop negative difference density after refinement if the site is of low occupancy, or if it actually is not a water site. These problem waters can easily be found with the validation tool and then deleted.
This tool displays a dialog box of the currently open maps and allows you to choose the map for the bones and RSR calculations. If there is only one map, this tool does nothing. If you select Quit, the map selection does not change. If you select OK, the new map is used for subsequent bones and RSR refinement calculations. The newly calculated bones will appear immediately.
This option displays the X-AUTOFIT Options dialog box, which is described on page 204, after the Finish option of the X-AUTOFIT:X-BUILD palette.
The Color table is described on page 211.
This tool allows you to save the Ca trace built in X-AUTOFIT/CA Build to a MSF file. It does not save information about the X-AUTOFIT all-atom model. This is not normally required, as all Ca trace information is saved in a session file. All residue names are saved as assigned in X-AUTOFIT | Sequence, so if Ca atoms have fuzzy descriptions, these will be saved as described. These residue names will not be recognized by most other graphics programs. To load the coordinate information from the MSF file created by this tool, use the tool X-AUTOFIT | CA Build | Load CA coordinates.
This tool allows an explicit save of the model built in X-AUTOFIT | Build atoms and X-AUTOFIT | Structure, and any coordinates generated by the tool X-AUTOFIT | CA Build | Fit seg by RSR. This is explicit save of data is not normally necessary as X-AUTOFIT will record any changes to a structure in the molecular management table, and force a save of the coordinates on exiting X-AUTOFIT.
The tool will bring up a dialog box that allows the generation of a new version of the file, save to a new filename, overwrite the file, or abort the save (see Finish, below). The molecule that is saved by this tool is the first active displayed molecule in the molecule management table.
The Save built atoms to PDB tool will save all the currently active and displayed molecules in the molecular management table to a single PDB file. The tool can be used to merge data into a PDB file for analysis and editing. If there are no active and displayed molecules, then only the symmetry cards are written to the file.
This provides a script-based interface to run external programs. The documentation on this is found later in this chapter (see External program palette).
The last command documentation is found at the end of this chapter (see Last commands).
The Finish tool will exit X-AUTOFIT and return you to main QUANTA and the modelling palette. On exit from X-AUTOFIT, the application will ask if you want to save any coordinates that have been changed in any way. If multiple MSF files have been changed while in X-AUTOFIT, this dialog box will appear for each MSF changed while in X-AUTOFIT. All molecules not edited are not saved on finishing. A dialog box is opened that allows various saving options:
The fourth option, to abort, has the same effect as Cancel, and returns you to X-AUTOFIT. The first three options, followed by OK, will result in the requested action on the MSF, and then a query about the next changed MSF. X-AUTOFIT exits after the last MSF save action.
If you do not wish to exit X-AUTOFIT, use Cancel.
The parameters in this dialog box control the general behavior of various tools in X-AUTOFIT.
This allows the choice of the Ponder & Richards library of geometries, the use of the Sutcliff library of geometries or the use of the Oldfield library of rotamers. This option effects the XAUTOFIT | Build atoms | Geometric conformation tool and the tools for placing side chains by dead end elimination (X-AUTOFIT | CA-build | Fit seg. by D.E.E and X-AUTOFIT | Structure | Fit by D.E.E). If the Ponder & Richards or Oldfield library is active, then the tool X-AUTOFIT | Build atoms | Geometric conformation will create a pop-up palette that contains each of the rotamers allowed for the selected residues, and sort these in order of likelihood. If the Sutcliff library is active, then only a list of the allowed rotamers is shown on the palette.
This allows you to choose the build mode for protein residues at a terminus ((X-AUTOFIT:X-BUILD | Build atoms | Add-delete | Add res at termini). Pfit is used to fit the terminal residue by fit to electron density, while the other choices define a geometric conformation.
This allows the choice of the build conformation when using the add residue at terminal for nucleic acids.(X-AUTOFIT:X-BUILD | Build atoms | Add-delete | Add res at termini). The initial conformation of the added residue is defined by the set of backbone torsion angles that define the option type.
This toggle changes the return set of dials after any edit in the X-AUTOFIT:X-BUILD tools. The default is to return the pointer dials after using a X-BUILD tool, for example: edit chi angles. If this toggle is set then the main dials are returned after an edit that changes the dial set.
This option affects the treatment of disordered residues. When it is turned on, it results in all conformations being superimposed onto the main chain atoms of the edited conformation on completion of editing by a tool. This means that when a residue A conformation is edited (for example, regularized), then on completion of the edit, the B conformation moves to the equivalent edited position, relative to the main chain atoms of the A chain. You should use clamping of the B conformer to the A conformer for all single residue disorder, and only turn off this option when a disordered loop is being added. The aim of this tool is to retain the main chain atoms as single atoms in a disordered residue, while allowing editing of the residue side chain of both A and B conformers.
This tool changes the effect of picking the Ramachandran plot window. When the toggle is on, you can pick a Ramachandran point in the plot window and the residue information is written to the Textport, and the center of the display will move to this residue. If this option is not set, then only the information is printed in the Textport and no centering of the screen is made.
The Ramachandran range option allows you to specify the number of Ramachandran points to be displayed in the Ramachandran plot window. This option is also defined for nucleic acids and the data values relevant for this type of polymer.
The default segment type is * and is all segments in the first displayed and active molecule. The start and end fields represent the limiting values of sequence number (resID) that are displayed in the Ramachandran plot. Note that the Ramachandran angles for the start and end residue are not displayed because of incomplete data for these residues.
The optional value (default 3.00 Å) sets the distance under which bumps between atoms are displayed. This option affects many of the build tools. When toggled on, X-AUTOFIT will show all the bumps (shorter than the specified distance) as white lines with the bump distance labeled at the center of the line between the bumping atoms. You may need to turn off the bumps if you are making large changes to the structure and the bump markers obscure the molecule.
This toggle option allows you to determine whether the bumps will be shown from edited coordinates to coordinates of MSF files that are inactive in the molecule management table. For example, if one open MSF file contains the coordinates that are being edited in X-AUTOFIT | Build atoms and a second molecule is open that contains coordinates from the last build as a comparison, then you will want to turn this toggle Off, because bumps to the last built coordinates are not relevant-they are only used as comparison coordinates. If other molecules in the management table are other parts of the same structure, such as ligands and water molecules, then this option should be turned On, so that bumps are always observed even when these are inactive. Note that bumps are not drawn to atoms not displayed.
Goes to the real atom when you pick a symmetry atom.
This toggle changes the behavior of the application when symmetry atoms are picked for the purpose of placing the center of the view with the tool Pointer | Place using coord. When this toggle is set to FALSE, the application places the center of the display (plus the bones and the map) at the symmetry atom picked. When this tool is set to TRUE, any symmetry atom picked when using the Place using coord tool will not place the display at the symmetry atom coordinate but at the real parent atom of this symmetry atom. This can be useful when a symmetry-related residue has been found to be in the incorrect position: the actual residue can immediately be found with this tool and then edited. The Symmetry picking mode tool can also be used with NCS, so that when both molecules related by NCS are displayed as real atoms, the NCS atoms will overlay these real atoms. Any differences (where the NCS has broken during the refinement if only partial constraints or restraints have been used) can immediately be observed. You can then jump back and forth between the two copies of the NCS when this option is set TRUE.
The next residue step allows you to set the increment/decrement for the tools Pointer | Place at next residue and Pointer | Place at previous residue. If the step is set to 2, the placement tools will jump along the polypeptide chain, missing alternate residues.
This tool allows the specification of the number of decimal points (DP) used on the non-bond contacts markers.
This has three possible options: None, Polar, and All. When you first start X-AUTOFIT, it checks the first few residues and sets the default hydrogen representation so that it matches them. If there are no protein residues yet built, or you wish to change the hydrogen representation, use this parameter to specify the mode you want.
Many tools on the Build palette cannot be used on residues that have incomplete or incorrect atoms, and this includes hydrogen atoms. If you change the hydrogen mode, then only the XFIT | Build atoms | Geometric conformation and XFIT | Build atoms | Fit side chain by RSR are allowed. These tools will build the residue from scratch, adding all the atoms and their correct names. You should use Edit | Split & Clean to change the hydrogen representation if there are many residues to change.
This option sets a default maximum search time for any of the "open ended" search algorithms within X-BUILD and X-LIGAND. These are the loop search in X-BUILD, terminal fitting in X-BUILD and the conformation search in X-LIGAND. The default time limit is 10 minutes, and, on reaching this time, the search will abort and provide a prompt box to continue, or finish the search.
This option sets the number of steps (cycles of refinement) used for the regularize tool under X-BUILD | Build-atoms | regularize. For a small number of residues the number of cycles of regularization is usually limited by the tolerance of minimization.
This sets the optional restraint towards certain conformations normally found in proteins. The actual value of the restraint is very low. Regularization will take much longer to converge with this option set to any value other than None. All residues being regularized will have their Ramachandran angles set to the conformation requested by this option, so large changes in the atom positions can occur if the starting conformation is a long way from the requested value.
The None option turns off phi psi restraints, so these torsions are free to take any value that quenches the deviations from ideality for bonds, angles, impropers, and active non-bond interactions.
The Helix option refines phi and psi values towards ideal helical values, the Strand option will refine phi and psi values towards those found in an ideal beta sheet, and the Nearest option will refine the phi psi values to the phi psi value nearest to the starting conformation, as defined from the Ramachandran allowed regions.
This option allows you to specify the required omega torsion that defines the peptide bond. The Auto option will first check to see if the peptide bond is in a trans or cis conformation, and then set a restraint towards the nearest ideal conformation. If a cis peptide bond is found by the regularization tool when in "auto" mode, X-AUTOFIT prints a warning to the textport.
The Trans and Cis options force peptide bonds to the specified conformation. Note that all peptide bonds in the regularized zone will be set to the requested conformation. Therefore, if a single peptide link is required to be in a cis conformation, then only regularize the two residues that make up that bond. During this process, some distortion occurs, due to large changes of atom positions. To correct for this, change the restraint to auto and regularize the region again. The auto detect will flag this as a cis bond and regularize towards it, while retaining all other peptide links as trans.
The default for this option is None. Normally regularization should be considered a method to improve the geometry of a section of the structure as a function of the bonds, angles, and impropers. This option allows a full nonbond description to be used, including atoms not involved in the regularization (such as symmetry). You can turn on full nonbonding for the regularization protocol, but this slows down the calculation, will make interactive modeling difficult due to the decreasing refresh rate. Also, the inclusion of nonbond interactions makes the interactive regularization less responsive because refinement will not go to completion during each step of the interactive editing. The recommended procedure is that you should not use nonbonding for interactive modeling of structures, but only for X-AUTOFIT | Build atoms | Regularize.
There are three nonbond modes, for all crystallographic protocols the push function is the suggested mode. The VDW and VDW | E modes use a full energy function terms for the nonbond interactions, resulting in slower minimization. For crystal structure modeling no advantage is obtained using the full functions, and in fact they do not minimize well as the potential surface is complex for these terms.
If this option is active, regularization (including X-AUTOFIT | Structure | Refine zone) will check to see if there are any cystine residues in the sequence before it proceeds. If there is a cystine then a check is made of the presence of a disulfide bridge to another cystine residue. If the other cystine residue is already contained in the regularize zone, then the parameters for this bridge are added to the parameters to be regularized. If the second cystine of the pair is not in the zone to be regularized, it is added to the list of residues for regularization and the bridge parameters are added to the list. If this option is not active, cystine residues do not receive any special treatment.
The coordinate radius sets the display radius about the current screen center for all the MSF files currently open. This is to allow very large structures to be manipulated on machines with poor graphics. We recommend that the coordinate radius should be at least 20 Å and larger than the map radius. If the coordinate radius is set to a value larger than 999 Å (the default is 1000 Å), then no checking of the atoms is carried out. This slightly improves the performance of the program when re-displaying a new screen center for structures where all atoms are required to be displayed.
This radius value is in effect for any subsequent map calculations or bones calculations. The display immediately changes to the new map radius after a new value is input. The default value is 6Å, which is recommended for less powerful computers. This value is saved in the session file.
The display will immediately change to the new symmetry calculation radius after you input a new value for this parameter. All symmetry atoms within the defined radius will be displayed. The default value is 10 Å. This option's value is saved in the session file.
The resolution factor is used in the real space refinement protocol, and will result in automatic adjustment of occupancies as a function of how far away a side chain amino acid atom is from the Ca atom. The further the distance from the Ca atom, the lower the occupancy. For all resolution factors less than or equal to 2.0 Å, there is no change in the occupancies of any atoms. For resolution values greater in value than 2.0 Å, there is an increasingly steep sliding scale of occupancies as a function of distance from the Ca. A value of 3.0 Å will affect medium and large residues to some degree, while a value of 4.0 Å will have a sizable effect on the occupancy at the end of a side chain. The purpose of the parameter is to lower the weighting during refinement of those atoms further from the main chain, in areas where the density is probably of poor quality. This prevents those atoms away from the main chain from pushing the main chain atoms out of density, or wrapping around towards the main chain during refinement. This option has no effect on the actual MSF. The values of occupancies are only changed during the refinement procedure.
The Color table tool opens a palette that allows the colors and line thickness of all the objects generated within X-AUTOFIT and X-BUILD to be changed. The changes made in this table are saved between sessions. The values here can be used to make an object stand out if you are working with a particular piece of functionality. For example, the default "moving object" color and width is often insufficiently distinctive during editing of a molecule. You can change this option using the Color table.
There will be between 0 and 6 lines of "map" object labels. Each map label will have 1 Width field and between 1 - 7 Color fields, depending on the number of contour levels defined for this map. This Color table makes changing the color and line width of maps very easy, but can only be used on open maps. The default values are zero line width and color 14, then 13, and so on.
The Bones main fields allow you to change the line width and color of the bones object that X-AUTOFIT considers to be part of the main chain. The default values are: line width = 3 and color = 6.
The Bones side fields allow you to change the line width and color of the bones object that X-AUTOFIT considers to be part of the side chain. The default values are: line width =3 and color = 5.
The Symmetry fields allow you to set the color and line width of the symmetry atoms. The symmetry atoms include the "all atom" symmetry, the Ca-trace symmetry, and bones symmetry. The default values are: width = 3 and color = 2.
The NCS fields allow you to set the color and line width of the NCS atoms. The NCS atoms include the "all atom" NCS, the Ca-trace NCS, and bones NCS. The default values are: width = 3 and color = 3.
The CA trace fields allow you to set the color and line width for the Ca trace display generated in the CA Build palette. There is a single line width value that sets the line width for all parts of the Ca trace, and three color values for different parts of the Ca trace.
Atom is the color used for the Ca-trace atom that is defined as the current atom. The current atom is the editable atom within the application. You can set it using the tool CA build | current res-seg.
seg is the color used for the current segment in the application, and is used for all the atoms in the current segment, not including the current atom. The current segment is set using the tool CA build | current res- seg.
rest is used for all Ca trace atoms in the application that are not the current atom or current segment. The default values are: width of 4, colors = 4 (red), 3 (yellow), 1 (red).
Only the color of the text labels can be changed, as the text labels have no line width. The text labels are the character strings generated using the Text... palette, and by the validation routines within the X-AUTOFIT: X-BUILD application. The default color = 4.
The Mask fields correspond the map mask dot surface generated in the Map Mask... palette of the X-AUTOFIT: X-BUILD application. The default values are: width = 2, color = 5.
The Vectors fields correspond to the objects generated as part of the application X-POWERFIT. These vectors indicate the major axes of the helices and strand elements found in the electron density map. The default width is 5, and colors 5 for helices and 10 for strands.
The Moving atoms field sets the color and line width of any temporary object generated during an edit function in the X-BUILD application. For example, the objects generated by Build atoms | Move zone. The default values are: width = 3, color = 5.
The Pointer fields determine the color and line width of the rhombohedral pointer used throughout X-BUILD and X-AUTOFIT. These Pointer settings also control the appearance of the spherical mask pointer. The default values are: width = 3, color = 5.
This opens the last command table where all the X-BUILD editing history is stored. The table can be used to check the progress of the model building process, undo and redo each command, analyze the work carried out, and create log files of the use of the X-BUILD functionality
To hide the table, pick the Last command tool again. Whether the table is present or absent does not effect whether commands are saved to the file. As each command is issued (and as the user accepts the changes made by that tool), data is added to the top of the table.
The last command table has a menu bar that contains tools for processing current and previous sessions of commands.
This writes a log file to disk, although this is automatically done on exit from X-BUILD unless command saving is completely turned off.
Command log file - written by Quanta: X-BUILD
Written at : 16:09:47 on Fri May 29 1998
Index Command Residue-range time : date
1 Save changes(*) A : 1-E : 6 15:25:09 on Fri May 29 1998
2 Save changes(*) A : 1-E : 6 15:31:33 on Fri May 29 1998
Comment -> (1) bad fit to density
3 Save changes(*) A : 1-E : 6 15:43:44 on Fri May 29 1998
4 Regularize A : 4 15:54:28 on Fri May 29 1998
5 Goto pointer(+) B : 26 16:01:32 on Fri May 29 1998
This will turn off all saving. To turn the saving back on again the user should pick the last command tool again on the main X-AUTOFIT X-BUILD palette and the application will prompt whether command saving is to be turned back on.
This tool will open a scrolling list of previous session files. The list contains multiple entries as:
(n) commands: (time written on date)
The list is sorted by date/time written, where the current open file is read/write and is first. All previous files are READONLY.
You can open the previous file and look at the contents in the table, You can also do analysis, undo/redo etc. to see what you did in previous session. However, you cannot write a tool entry to any READONLY previous command session file. If you use a new tool, the previous file is closed, the current file is reopened and the tool entry added to the current session file.
This tool lets you delete old files or just delete all the old session files. A scrolling list is shown, and each entry can be kept or deleted. This command moves all session files down one to fill any gaps.
This tool controls whether info lines with (+) at the end of the tool name are hidden.
This tool controls whether the molecule display is labeled with the user comment cards added.
This will return the percentage of each tool usage in a table to the text port.
This will make simple suggestions as to the usage of X-BUILD as a function of the tool usage.
The last command table contains seven columns of data that summarizes the changes that have been made to the coordinate model by editing coordinates with an X-BUILD function:
By default, the table is sorted by Index so that the last command is at the top of the table, but the tables can be resorted by picking the column headers Command, Residues, Time, Comment, so that it is possible to collate the tool usage differently. Note that clicking the Residue column sorts the table using the first residue within the edit range. If either the Undo or the Redo headers are clicked, then the program prints out an analysis of the commands used within the X-BUILD functionality and makes suggestions to the tool usage.
It is possible to pick cells within the last command table, and picking a cell results in an action defined by the column the cell belongs to. If a cell in the Command column is picked, then details of the changes made during the edit are printed to the text port. This information includes the RMSD, max and min atomic deviation per residue. If a residue cell is picked, then the program centres the display at edited residues for the particular command and moves the pointer to this position. If a Time cell is picked, then a full time/date record is written to the text port, where the table only shows the time information due to space limitations.
If the Redo or Undo cells are picked, you can redo and undo each tool edit as required. Note that the data stored for each edit consists of the coordinates (and temperature factors/occupancy) for each atom before and after the edit. Therefore an Undo modifies the coordinates so that the change made is undone. The Redo cell modifies the coordinates so that a particular edit is redone. Note that if multiple edits have been made to a particular residue then the last edit can only be redone from the last edit of that residue, and all edits to a residue can only be recovered from the first Undo of the first command containing this residue. Additionally the changes to a residue can be studied at all the intermediated edits.
The command cell, when picked, allows you to add a comment that is relevant to the edit made. This comment is written to the log file of the build session, and can also be displayed on the structure view using the menu option (see below).
The menus allow you to open a previous last command table from an earlier model building session. When this is the case, all the cell picking is active and can be used to recover changes made at an earlier date. New edits to the structure are not added to a previous command table, but the current version is reloaded and change added to this.
The last command table therefore stores all the edits and details about these for an entire build session. This command table allows point in time data recovery, data analysis and a note book facility. It is also possible to use the last command table as a teaching aid as it can be set up to show best practice for map fitting.
This palette, when no script files have been written, contains only the hide this menu tool. Tools will only appear on the palette if correctly formatted scripts have been written.
Scripts must have names script.# where # is a number between 1 and 20.
A script file is an ascii file of key worded instructions that defines the layout of a dialog box and the generation of a command file to run a particular external program. The script files also contain control key words to export coordinates from X-BUILD, and also to import coordinates and maps back into X-BUILD. The aim of script files accessed from the External program palette is to set up an interface to external programs allow you to run them directly from QUANTA. The script defines the layout of a dialog box, including hidden preference boxes and, using the data entered in the dialog box, runs an external program with the parameters defined by the user.
The scripts can be changed when the dialog is not visible as each script is only read when the dialog box is opened. A debugger is provided when the script is interpreted to provide some feedback on the generation of the script.
Script: file containing the described information in this help that defines the look of a dialog and the contents of a command file.
Command file: file produced by a script that is submitted to be run by the computer, and is normally (but not necessarily) an external program command file.
Program (program name) (Text string description of program)
< assignments of variables >
< control statements >
< QUANTA data export statements >
< script definitions for dialog and command file >
< QUANTA data import statements >
Only the program name and description is required, although other statements are necessary for a meaningful script.
Variables within scripts can be defined and can either be text or number values, no distinction is required. A variable can be initialized using the assign keyword, or are taken from a dialog entry box.
A text string without spaces can be added to a script as is, but text strings containing spaces or commas much be enclosed by double quotes to delimit the string.
All fields are required - an empty text field can be placed with " "quotes; note that a space is required.
A text string delimited by { } curly braces defines a variable in the script that will be replaced by the value of the variable when used.
All short fields are, by default, un-initialized variable names for the entry field they specify.
This line is the only required line and must be the first line of the script. The keyword is program, and the first parameter is a text string that is written at the top of the dialog box while the description text is not used.
Initialized variables are set using the line:
assign data "input_data"
The name of the variable is (data) and its initial value is a text string (input_data). This variable can then be used with a command file line as:
write "FILIN {data}" (The write keyword writes the line as is to the command file).
The variable can also be used to define the initial state of a dialog input:
string 1 "Input" "File" "{data}.pdb" "Input PDB file" format 40 (The string defines a dialog string input).
Uninitialized variables can be used when their value is defined from a dialog entry field when the OK button is clicked. Generally they can only be used in a command file line:
write "calc u(100) = {Bond}" The quoted string here is written to a command file when the dialog OK button is clicked, and the value of the variable bond is taken from a dialog entry value. Make sure the variable is defined or nothing will be written.
An example dialog entry field to define this variable:
dreal 1 "n7" "Bond" 0.10000 "Warning limit (A)"
The dreal keyword defines a dialog only entry field (does not provide output to a command file - hence can only be used to set a variable), and the variable "Bond" is defined by the short string label for the real entry field whose initial value is 0.1.
Variables can also be used for hidden dialogs such a preference dialog box:
dbutton 1 "n1" "Preferences" " "
dif {Preferences} then
dreal 1 "n7" "Bond" 0.10000 "Warning limit (A)"
dreal 1 "n8" "Angle" 5.0 "Warning limit (o) "
dendif
This example shows a dbutton keyword defining a dialog only field button with the short name of Preferences. The dif keyword defines a dialog only condition statement that will display the contents of the dif - dendif statements as a dialog if the dbutton Preferences is pressed. (The contents of the preference box would contain two dialog-only real entry fields to define the value of the variables {Bond} and {Angle}).
The control statements define the general behavior of the dialog and command file submission.
saveall
saveOK
savecancel
nosave
These four control statements are used to define whether the contents of the dialog entry fields are remembered when the dialog is exited. The normal default would be to saveOK, where the contents of the dialog fields are written back to the script file when the dialog OK button is pressed. Hence, the value of the dialog entry fields are remembered when the user wants to carry out the action (to run the command file). "Saveall" will always save the entry fields; "savecancel" will only save the fields if the "cancel" button is pressed, and "nosave" will not save the value of the entry fields back to the script.
notify
The notify control statement will write a <Crtl> G to the end of the command file, so that the completion of the command file will result in a beep.
nowaitwait
The nowait control statement results in a submission of the command file and immediately returning control to QUANTA. This option is sensible when the calculation performed by the external file takes some time. The default wait statement pauses any action in QUANTA until the command file action has completed.
#
The # character as the first character on a line is used to define a comment line, and any subsequent text on the same line is ignored.
There is currently only one data export statement output, though the format allows future additions. If the dialog OK is accepted, all output statements are carried out before the script is run regardless of their placement in the script file. It can therefore be assumed that the filename produced will exist when the command file is submitted to be run.
output pdb (filename).
The output statement is followed by a format (in this case pdb - a file of coordinates in PDB format for active and visible molecules in QUANTA/X-BUILD). No other formats are currently allowed.
The filename is the file name of the output coordinates.
There are currently only two data import statements, though the format allows future additions. If the dialog OK is accepted and a wait control statement is provided, all import statements are carried out after the script is run regardless of their placement in the script file. If a nowait control statement is placed in a script with an import statement, the imported information will be undefined.
import pdb (filename)
The import statement is followed by a format (in this case pdb). The imported coordinates will replace the currently active and visible coordinates in QUANTA/X-BUILD. It is necessary that the number of atoms, the atom names and size of residues exactly matches that of the QUANTA data structure.
import map (filename)
The import statement will open a QUANTA brick map of name (filename).
The order of the script definitions defines the order they appear on the dialog and also the order of the lines of text in the command file. It is generally most efficient to use definition keywords that define both the dialog and command file, though this sometimes is not possible -- hence the use of variables.
Script definitions can be divided into three categories:
1. Those that control only the structure of the written command file.
2. Those that control only the structure of the dialog.
3. Those that control both the dialog and command file.
There is only one keyword that controls the command file; this is used to write a string of text (including numbers) when the command file is generated. It is possible to use variables in the written text to enter variable values defined from the dialog entry fields or assignment statements.
write "a string of text {including} variables" The text string in quotes is written as is (except for the variables) to the command file.
Dialog only statements define the layout and field entry within the dialog and have no effect on the generation of the command file. They can be used to set the value of variables or to generate hidden dialog boxes. There is no reason to create a dialog only field entry that does not define a variable. All dialog entry fields implicitly define variables for each entry field. The variable name is the "short string" of the field. All statements are free format.
Except for the space keyword, the general format of a dialog entry field is...
(keyword) (Nfields) (Command string) [ (short string) (field default) ] (long string) (format fields)
The following are the allowed keywords.
dreal 2 "bond-angle" "Bond" 1.0 "Angle" 2.0 "Parameters:" format 8.3
A two field real number entry dialog string where the initial value of the bond entry is 1.0, the initial value of the angle entry is 2.0, and the format of the entry field is f8.3. The look of the dialog would be a line.
Parameters: Bond [ 1.000 ] Angle [ 2.000 ]
For example: A hidden box (note that there is no default value field here):
dbutton 1 "hidden-box" "" " "
dif {Preferences} then
dreal 2 "bond-angle" "Bond" 1.0 "Angle" 2.0 "Parameters:" format 8.3
dendif
The dbutton entry line defines one button labeled Preferences and no preceding long string name as indicated by the empty quotes.
[Preferences]
The hidden box contains the line in the previous example. When the button is pressed, the current dialog is replaced by the hidden dialog box (a single line with two real entry fields here), and a single [return] button to exit back to the parent dialog box.
Note: Nested dialog boxes are not supported.
These statements are the most useful to create scripts as they control both the dialog and command file. They have exactly the same format as dialog only lines. Not only can these statements control the look of the dialog and the command file, the fields can be used a variables, but this may result in multiple use of a field. All statements are free format.
(keyword) (Nfields) (Command string) [ (short string) (field default) ] (long string) (format fields)
The following keywords are valid:
option 3 "REFI METHOD" "CGMAT" T "CDIR" F "CGRADD" F "Refinement method" xstart 2500 xsep 1500
Format additions are added to a dialog definition that change the look of the dialog box for a statement. They have no effect on the command file.
Format (n):(n) depends on string/integer/real fieldsxstart (n): Start point of the fields in 1/1000 inch xsep (n): Separation of the fields in 1/1000 inch append: Place current statement fields at the end of the previous statement fields vertical: Place each field entry on a new line - vertical arrangement
For integer field, format 4 would allow a four character integer number entry from -999 to 9999.
For a real field, format 8.3 would allow a eight character number entry with up to three decimal places.
For a text string, format 20 would allow a twenty character string entry/
It is possible to add a continuation mark to the end of a line in the command file by adding a "/" at the end of any statement line. This does not affect the dialog box.
1. The following example creates a single text entry using a dialog only statement and a variable {file} to pick up the user defined name for the export statement. (Note that the {file} variable is the short text name for the text entry field. By default the file name is updated in the script when [OK] is pressed. (i.e., default "saveOK")
program "Write PDB" "Write of displayed/active molecules"dstring 1 "n1" "file" "script.pdb" "PDB name" xstart 2500 xsep 2500 format 40.00 output pdb {file}
2. The following script was used to run the program SQUID for the validation of proteins. This external program functionality has now been replaced by the Tables and Graphs functionality within QUANTA and is therefor no longer provided.
program squid "Squid Validation"
wait
assign strdir "$HYD_LIB/squid/"
output pdb script.pdb
write "#!/bin/csh -f"
write "setenv SQUIDIO /y/programs/squid/squidio"
write "$HYD_EXE/squid -none -file script.pdb -put 300 300 700 700 << `END'"
write "echo"
write "check"
write "xfit open"
write "sel resi protein"
write "excl atom h* d*"
write "calc u(100) = {Bond}"
write "calc u(101) = {Angle}"
write "calc u(102) = {Plane}"
write "calc u(103) = {Clash}"
write "calc u(104) = {Probe}"
write "calc u(105) = {Water}"
label "Refinement parameter check"
toggle 1 "stream {strdir}check_restraints.str" " " TRUE "Check bonds etc." xstart 2500 xsep
toggle 1 "stream {strdir}check_HNQ.str" " " TRUE "Check HNQ" xstart 2500 xsep 2500
toggle 1 "stream {strdir}check_cis.str" " " TRUE "Check for cis peptides" xstart 2500 xsep 2500
toggle 1 "stream {strdir}find_holes.str" " " TRUE "Check for possible voids"
toggle 1 "stream {strdir}check_clash.str" " " TRUE "Check for clash" xstart 2500 xsep 2500
dbutton 1 "n1" "Preferences" " "
dbutton 1 "n2" "Don't press this !" " "
dif {Preferences} then
dreal 1 "n7" "Bond" 0.10000 "Warning limit (A)"
dreal 1 "n8" "Angle" 5.0 "Warning limit (o) "
dreal 1 "n9" "Plane" 10.00000 "Warning limit (o)"
dreal 1 "n3" "Clash" 1000.00000 "Warning limit (Kcal)" xstart 2500 xsep 2500
dreal 1 "n5" "Probe" 1.2 "Voids Size (A) "
dtoggle 1 "n6" "Water" FALSE "Use water" xstart 2500 xsep 2500
dendif
dif {Don't press this !} then
space
space
label " Boo !"
space
space
space
dendif
write " "
write "xfit close"
write "end"
write "yes"
write "`END'"
1. Greer, J., J. Mol. Biol. 82, 279-301 (1974).
2. Oldfield, T.J., and Hubbard, R.H. Protein: Structure, Function and Genetics, 18, 324-337 (1994).
3. Ramachandran, G.N., and Sasisekharan, V. "Conformation of polypeptides and proteins", Adv. Prot. Chem., 23 283-437 (1968).
4. Dickerson, R.E., and Guis, I., The Structure and Action of Proteins, Benjamin/Cummings, ISBN 0-8053-2391-0.