Most of this chapter focuses on how to manipulate molecule displays in the viewing area. The chapter describes display choices, including how to display and label complete or partial images of a structure and how to customize atom, label, and bond colors. It also includes how to select subsets of the atoms in your structure for calculations.
No manipulations described in the display sections of this chapter affect basic structural information used in modeling operations or calculations. Display manipulations do not affect this information in an active molecular structure or in an MSF on the disk.
In contrast, the Selecting active atoms section of this chapter describes methods for selecting some or all parts of a structure for modeling operations and calculations. These procedures do affect structural information used in modeling operations and calculations. They operate on the set of atoms contained in an active molecular structure, but not on the information contained in the disk-stored MSF. If you want to store a new information set you create through the active atoms selection process, you should save it to a new MSF.
Displaying a structure with selected active atoms may appear similar to displaying a structure where some atoms have been masked for visual purposes, but these two functions are actually very different. Do not confuse them.
This chapter assumes you have already run QUANTA. If you have not, refer to Starting QUANTA in Chapter 1 for information about initial startup.
To continue work on the exercises included in these QUANTA introductory books after subsequent start-ups, enter the command:
> cd ~/accelrys_quanta
> quanta
QUANTA opens by displaying the structure PEPTIDE.msf in the viewing area. The Molecular Management table displays the structure's name and status.
If you are opening QUANTA for any other purpose, do so in another subdirectory using the same procedure. The interface will show the last structure displayed in the previous session in that subdirectory.
You can display some or all atoms of a molecular structure in the viewing area. By using masking to filter atoms, QUANTA helps you visually focus on one area or aspect of a structure. Meanwhile, any calculations that are performed include all atoms in the structure.
Display Atoms in the Draw menu is used to determine which atoms are selected for viewing. Atoms in a structure can be displayed using the predefined choices in the pull-right menu, or by choosing Selection Tools in the Display Atoms menu to bring up the Display Atoms and Display Utilities palettes. Using palettes takes more steps but gives you more flexibility in tailoring your display.
Selections in the Display Atoms pull-right menu are those used frequently. See Table 12 for a list and description of these selections, which display only the atoms matching the specified category. For example, you can select Protein Backbone and have only the atoms in the backbone displayed.
The Display Atoms palette includes the same display selections as the pull-right menu plus additional choices. Some selections result in automatic displays. Some require you to make additional selections. Table 13 lists all palette selections and provides a short functional description of each.
When you make a selection from the Display Atoms palette, the resulting display is in two colors. Default colors are blue for unselected atoms and red for selected atoms. When you first open the palette, all atoms are in blue (unselected), regardless of previous selections. You can revert to your previous selection by using Revert on the Atoms Display palette.
To help verify a selection, check the number of atoms listed in the Displayed column of the Molecule Management table. All atoms in a structure, whether selected or unselected for display, are included in calculations for the structure. Display selections are stored in a .dsf file.
After you have selected the portion of a molecule you want to display, make choices from the Display Utilities palette to view different aspects of the selected portion of the molecule.
See Table 14 for a complete list and description of the Display Utilities palette selections. If you have more than one MSF displayed, you can define separate criteria for displaying the atoms or structure within each MSF. For example, you can choose to display all the atoms in one structure and the backbone of another structure.
|
Mark Selected Atoms
| |
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Mark Unselected Atoms
| |
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Color Selected Atoms
| Displays selected atoms in color 3 (default is red). Displays unselected atoms in color 2 (default is blue). |
|
Display Selected Atoms
| |
|
Read Selection Commands
| Reads commands from file.dsf and updates the viewing area to reflect the new set of commands. |
|
Append Selection Commands
| Appends to the current file, .dsf, with a set of commands from another file, file.dsf, and updates the viewing area to reflect the new combined set of commands. |
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Save Selection Commands
| Saves the current set of commands to a new .dsf. Only available when One MSF is selected in the Display Atoms palette. Selections can only be saved for one MSF at a time. |
|
List Selection Commands
| |
|
Edit File Manually
| Allows a .dsf file to be manually edited. Opens a new window, which uses the vi editor by default for editing the file1. |
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Help on Commands
| Provides a list in the textport of display selection commands that can be used from the keyboard. Each entry includes a short example. |
|
1It is possible to change the default editor by using the setenv command before QUANTA is started. The syntax is: setenv EDITOR (name of system editor to be used).
|
Complete the following exercises to become familiar with the automatic display options.
1. Open the Display Atoms menu and make a selection.
In the Draw menu, select Display Atoms and open the pull-right menu.
Select C-Alpha Trace. The display of your structure becomes a light green trace line connecting the alpha carbons of the peptide.
Now select Protein Backbone from the pull-right menu. The C-alpha trace is replaced by a multi-colored display of the atoms that make up the protein backbone of PEPTIDE.msf. The textport and the Displayed column of the Molecular Management table report that 103 atoms are displayed.
2. Open the Display Atoms and Display Utilities palettes.
The molecule display reverts to all atoms. The Display Utilities and Display Atoms palettes appear to the right with their default settings checked and highlighted. The molecule changes color so that all atoms are blue, the default color for other unselected atoms.
In the upper-right corner of the viewing area, the words Selected and Unselected appear in blue and red respectively to remind you of the colors associated with display selections.
If you wish to start from your previous selection, please use the Revert tool.
The Displayed column of the Molecule Management table indicates that 0 atoms are displayed, and the Active column indicates that all atoms (201) are active.
3. Redisplay the peptide backbone
Select Revert from the Display Atoms palette. The protein backbone atoms of the peptide are selected and displayed in red. Other atoms remain blue.
4. Further customize your display
Select Display Selected Only from the Display Utilities palette. The display changes so that only the atoms in the backbone appear in the same colors as the protein backbone displayed after it was selected from the pull-right menu.
Now select Mark Selected Atoms from the Display Utilities palette. The complete peptide molecule is displayed, but the atoms contained in the backbone of the structure are now marked with purple asterisks.
Select Mark Unselected Atoms from the palette. The complete molecule is displayed, but this time, atoms not contained in the backbone of the structure are marked with purple asterisks.
Select Color Selected Atoms. The display returns to a red and blue display.
5. Exit without saving your selection
Select Quit from the Display Atoms palette. The screen returns to standard viewing mode. The protein backbone of the structure is displayed as it was prior to using the palette tools.
The Display Atoms and Display Utilities palettes also provide selections that establish specifications based on designated atoms contained in the displayed structure. Using these tools is a three-step process.
a. Specify if one or more atoms are to be included or excluded in a display by selecting either Include or Exclude from the Display Atoms palette. Include is the default.
b. Define the structural category represented by selected atoms by selecting a choice from the Display Atoms palette, for example, Pick Residue or Pick Segment.
c. Using the mouse, pick an atom in the displayed structure to designate the portion of the molecule to be affected by the selected structural category from Step b.
The practice examples below illustrate this process.
1. Exclude a range of residues from a selection
Display the Draw menu. In the Display Atoms pull-right menu, select Selection Tools. The Display Utilities and Display Atoms palettes appear to the right with their default settings checked and highlighted.
The peptide molecule is displayed in blue (default color 2) indicating that all atoms are unselected. The words Selected and Unselected appear in the upper-right corner.
Select Include and All Atoms from the Display Atoms palette. The entire structure is selected and displayed in red.
Select Exclude and Pick Residue Range... from the Display Atoms palette. Using the mouse, select a range of residues to exclude by picking any two atoms in the structure.
As you pick, each atom ID is displayed. All atoms contained in the residue range that you identify are now unselected and highlighted in blue. Information about the picked atoms and the number of atoms in the selection is displayed in the textport in a message such as:
Picked Atom: HZ1_SEG1:16 PEPTIDE.msf Residue Type: LYS
Picked Atom: CB_ SEG1:18 PEPTIDE.msf Residue Type: VAL
171 Atoms to be displayed
Choose List Selection from the Display Utilities palette. Information similar to the following is displayed in the textport:
The Current Display Selection is: PEPTIDE.msf
DATA
ALL
EXCLUDE
ZONE SEG1:16 TO SEG1:18
Select Pick Residue Range again to turn it off. Select Clear ID from the Geometry palette to remove IDs.
Select Exclude and All Atoms from the Display Atoms palette. The molecule is displayed in blue (unselected). Include is automatically selected.
Select Residue Type from the palette. A dialog box is displayed with a list of residues in the molecule.
The dialog box closes and all serine residues in the molecule are displayed in red. A message in the textport indicates the number of selected atoms in the display.
Repeat the process, this time selecting Arg in the dialog box. All arginines in the molecule are displayed in red along with the serine residues.
Select Include and All Atoms from the palette. The structure returns to an all-blue display of unselected atoms.
At any point during a selection process, it is possible to list the selection commands you have made thus far by choosing List Commands from the Display Utilities palette. The list is displayed in the textport.
If you select Proximity Tools on the Display Atoms palette, the Proximity Selections palette is opened. Selections on this palette allow you to display and study specific portions of the molecule and areas nearby.
When this palette is open, proximity dimensions are listed in the lower-right corner of the viewing area. For example, when you open the palette for the first time, information in the lower right corner of the viewing area reads:
Radius = 5.000 Å
This is the default radius set for all proximity selections.
With the opening of the Proximity Selections palette, Dial Set U opens in the dial emulator. The radius dial is displayed for controlling the radius of a sphere, the default for proximity selections. This and other dials displayed when proximity selections are activated work in the same manner as other translation and transformation dials.
Table 15 lists palette selections and provides a brief functional description of each. As in the Display Atoms palette, some proximity selections are predefined and some are interactive, allowing you to customize your selection. Interactive selections are multiple-step processes.
Complete the following exercises to familiarize yourself with the Proximity Selections palette selections.
1. Open the Display Atoms and Display Utilities palettes
Display the Draw menu. In the Display Atoms pull-right menu, select Selection Tools. The Display Utilities and Display Atoms palettes appear to the right with their default settings checked and highlighted.
2. Clear all previous display selections
With the Display Atoms palette open, select Exclude and All Atoms. The structure is displayed in blue.
Select Proximity Tools from the Display Atoms palette. The Proximity Selections palette opens. Proximity parameter information is displayed in the lower-right corner of the viewing area.
3. Make proximate atoms selections
The picked atom ID is displayed. All atoms within 5.0 Å of the picked atom are selected and displayed in red. The textport displays information about the picked atom and reports the number of selected atoms.
Return to the palette and select Around Residue. Using the mouse, pick a new atom to select a central residue.
The new atom ID replaces the previous selection, and a new set of proximate atoms is selected and displayed in red. The textport lists information about the new picked atom and reports the total number of selected atoms in the structure.
Choose Clear from the palette. All selected atoms are removed and the entire structure is displayed in blue. Select Clear ID from the Geometry palette to clear the viewing area of IDs.
4. Use a graphical object to select proximate atoms
A cylinder appears in the viewing area. In the lower-right corner, the default radius (5 Å) and length (5 Å) of the cylinder are displayed.
Select Set Object Origin from the palette, then use the mouse to pick an atom to be the origin around which the object is centered.
An ID is displayed and the object becomes centered around the atom you picked. The textport lists information about the atom, and the message line reports the coordinates of the cylinder's origin.
5. Manipulate the graphical object and structure to examine the selected atoms
Use the Rotate X, Rotate Y, and Rotate Z dials to adjust the position of the cylinder around its center.
Choose Apply Selection from the palette. Atoms within the cylinder are selected and displayed in red. The textport reports the number of atoms selected.
Select Dial Set 1 at the bottom of the dial emulator. Use the dials on this set or use your mouse and keyboard to move your molecule and the cylinder so that you can see selected atoms within the cylinder from a variety of views.
6. Remove the graphical object
Click Graphical Cylinder again to deselect it.
The cylinder is removed from the viewing area, but the atoms remain selected and displayed in red.
Select Clear ID from the Geometry palette to clear the atom ID from the viewing area.
7. Exit the proximity function
Return to the Proximity Selections palette and select Exit Proximity. The palette is closed and proximity parameter information is removed from the viewing area. Selected atoms remain selected and displayed in red.
8. Return to molecular modeling mode
Select Include and All Atoms from the Display Atoms palette. The entire molecule is displayed in red.
Select Finish. The Display palettes close and the peptide is displayed in standard molecular modeling mode.
Visual feedback in a molecular study is often enhanced by highlighting specific atoms with color. QUANTA provides a variety of options for assigning color to displayed structures and to specific areas within a structure.
Atoms in an MSF, as well as hydrogen bonds, IDs, and labels, are assigned color numbers and default colors. Any default color assignment associated with a particular color number or with a particular type of atom, bond, or label can be reassigned. You also can change the color of a predefined set of atoms or any specific selection of atoms in a structure, and you can highlight different areas or characteristics of that structure.
If more than one MSF is displayed, you can define criteria for coloring the atoms within each structure differently or define criteria for coloring some portions of all structures the same way.
Atoms contained in a structure can be displayed in as many as 14 colors. In addition, one color is assigned to IDs and labels, and one is assigned to hydrogen bonds. These colors are defined using the Dial Emulator, Dial Sets 5 and 6, or by a variety of choices provided by the Color Definitions selection in the Preferences menu.
Table 16 lists the dials in sets 5 and 6, their assignments, and their default colors.
See Dial emulator for a basic description of dial emulators and their manipulation.
For the color dial sets, each dial has four parts:
The following exercise illustrates manipulation of the color dial emulators to customize the colors you use in your MSF displays:.
1. Display the first set of color dials
Move the cursor over the 5 in the Dial Emulator Selection box located at the bottom of the dial emulator. Click the left mouse button.
The first six atom color dials, and the color dials for labels and IDs (ID) and hydrogen bonds (HB), are displayed. By default, the color of dial 1 (light green) is assigned to the carbon atoms in the displayed structure.
Move the cursor to the left side of the H box of dial emulator 1 and click the left mouse button. The message line displays the current values of hue, saturation, and intensity for color 1.
With the cursor over H, press and hold the left mouse button.
The hue changes for both dial emulator 1 and the carbon atoms in the displayed peptide structure. The hue value, displayed in the message line, decreases to reflect the change in the display. When this value reaches zero, it automatically changes to 360 and decreases in value again. The hue of dial emulator 1 and the hue of the carbon atoms in the displayed structure continue to change relative to these values.
The hue of dial emulator 1 and the hue of the carbon atoms in the displayed structure continue to change. However, the hue value displayed in the message line is now increasing.
3. Define the saturation for color 1
Move the cursor to the left side of the S box of dial emulator 1. With the cursor over the S, press and hold the left mouse button.
The saturation changes for both dial emulator 1 and the carbon atoms. The saturation value, displayed in the message line, decreases to reflect the change in color. When this value reaches 0.01, it automatically stops. The saturation of dial emulator 1 and the saturation of the carbon atoms also stop changing.
The saturation of dial emulator 1 and the saturation of the carbon atoms resume changing. However, the value is now increasing. When the saturation value reaches 1.00, it automatically stops. The saturation of dial emulator 1 and the saturation of the carbon atoms also stop changing.
4. Define the intensity for color 1
Move the cursor to the left side of the I box of dial emulator 1. Press and hold the left mouse button.
The intensity changes for both dial emulator 1 and the carbon atoms.
The intensity value, displayed in the message line, decreases to reflect the change in color. When this value reaches 0.01, it automatically stops. The intensity of dial emulator 1 and the intensity of the carbon atoms also stop changing.
As you continue to press and hold the left mouse button, move the cursor to the right side of the I box.
The intensity of dial emulator 1 and the intensity of the carbon atoms resumes changing, however, the value is now increasing. When the intensity value reaches 1.00, it automatically stops. The intensity of dial emulator 1 and the intensity of the carbon atoms also stop changing.
Each atom display color also can be individually defined using menu selections. Selecting Color Definitions in the Preferences menu opens a pull-right menu that contains the selections listed and described in Table 17. In most cases, selections are predefined and automatically applied.
The All Definitions selection in the Color Definitions pull-right menu opens a Customize Color Settings dialog box with the selections listed and described in Table 18. Some of the selections in this box are identical to those on the pull-right menu.
Use the following exercise to become familiar with menu functions that define MSF display colors:.
1. Make a selection from the Color Definitions menu
Display the Preferences menu and select Color Definitions. A pull-right menu opens. Select Black and White from the pull-right menu. The MSF in the viewing area is displayed in black, white, and grey colors against a white background.
Select Reset All from the pull-right menu. The display returns to default colors.
2. Set hue, saturation, and intensity for an atom display color
The Customize Color Settings dialog box is displayed.
A dialog box is displayed and asks for the color number to be changed.
A dialog box containing data entry fields for hue, saturation, and intensity of color 2 is displayed. Each field contains the current value. By default, color 2 is blue and is assigned to nitrogen atoms in the displayed structure.
The color of the nitrogen atoms in the displayed structure changes to purple. Dial emulator 2, used to define color 2, also changes to purple.
The dialog box containing available color options for structures is redisplayed.
3. Define a color for a non-atom portion of an MSF display.
The atom should be located to the far right of the viewing area, so that it is not obscured by dialog boxes. The atom ID is displayed in the default green color.
Reopen the Customize Color Settings dialog box by displaying the Preferences menu, opening the pull-right Color Definitions menu, and selecting All Definitions.
Select ID/Labels from the dialog box and click OK. A dialog box containing data entry fields for hue, saturation, and intensity of ID/Labels is displayed. Enter the values 60, 1.00, and 1.00 in each successive data entry box. Click OK.
The color of the displayed ID changes to yellow. The dialog box containing available options for display colors is reopened.
4. Define a set of structure colors.
Atom and viewing area colors are changed to the CPK convention.
The dialog box containing available color options for structures is redisplayed.
5. Reset all colors to their defaults.
Display the Preferences menu and open the Color Definitions pull-right menu. Select the option Reset All. The viewing area and all structure colors return to their default values.
Move the cursor over the 1 in the dial selection box at the bottom of the dial emulator. Click the left mouse button. The color dials set is replaced by Dial Set 1.
The two types of color assignment options are automatic and user-defined. Automatic color assignment requires atoms to be specified by category, while user-defined options allow you to specify exactly the atoms or areas of a structure that you want to color according to various criteria.
QUANTA assigns color numbers based on your selections. The color number corresponds to one of the 14 colors for atom display. The actual color this number represents is defined by default or by adjustments you make using dial emulators or the Color Definitions function in the Preferences menu. For information on color definition, see "Customizing display colors" on page 75.
You make color assignments by selecting Color Atoms from the Draw menu. A pull-right menu contains several commonly used selections. These are listed along with brief functional descriptions in Table 19.
If you select Selections Tools from the pull-right menu, the Color Atoms and Color Schemes and Utilities palettes are opened and displayed to the right of the viewing area. In addition, Color Dials Set 1 comes up in the Dial Emulator window.
The legend *Color 2* is displayed in the top right-corner of the viewing area, indicating the color that will be applied to subsequent selections. The pull-right menu is dimmed and cannot be accessed again until the palettes are closed.
The Color Schemes and Utilities palette includes tools that assign subsequently selected atoms to be colored according to chemical or physical properties or according to atom location in the MSF, or color all structures according to molecule, segment, or bond order.
The palette also includes tools that set the display color values (default color, blue-to-red smooth range, red-to-blue smooth range, and user-defined smooth range). These selections are also available through Color Definitions in the Preferences menu.
A third category of tools on this palette is editing and filing. Table 20 lists the palette selections along with brief functional descriptions.
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Next Color Number
| |
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Choose Color Number
| |
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Color by Number
| Subsequently selected atoms will be colored using the color number defined using the first two tools. |
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Element Type
| |
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Atomic Charge
| Colors subsequently selected atoms in ascending order of charge value using the 14 atom color numbers. The display colors should be set to a smooth or tonal range when using this scheme. |
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Fourth Parameter
| Displays dialog box requiring user-defined input of a fourth parameter for coloring the subsequently selected atoms. The display colors should be set to a smooth or tonal range when using this scheme. |
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Property Value
| Colors subsequently selected atoms using the current property definition. (See "Atom property coloring" on page 89.). |
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Amino Acids by Polarity
|
Colors subsequently selected amino acid residues according to their polarity. Each residue is assigned a color number predefined in QUANTA. These assignments are: |
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Secondary Structure
| Colors each subsequently selected residue by its secondary structure type as defined in the Protein Design application. |
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Each Molecule a Different Color
| |
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Each Segment a Different Color
| Colors all atoms by segment. First segment color is Color 14 (default = pink), second segment color is Color 13 (default = orange), and so forth. |
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Color by Bond Type
|
Colors bond types with different color numbers: This selection overrides all other color assignments but is only available if bond orders are stored in the MSF. |
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Default Color
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Blue-to-Red Smooth Range
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Red-to-Blue Smooth Range
| |
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User-Defined Smooth Range
| Displays a dialog box that allows you to set up a customized spectral color ramp (varying fully saturated hues). |
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Blue to Red Tonal Range
| |
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User-Defined Tonal Range
| Displays a dialog box that allows you to set up a customized "electrostatic" color ramp (varying saturations). |
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Read Selection Commands
| Reads selection commands from a selection file, overwriting current selection commands and updating the viewing area. |
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Append Selection Commands
| Appends entries in a selection file to the current command list and updates the viewing area. |
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Save Selection Commands
| Saves selections to a file. Available only if the One MSF selection is checked on the Color Atoms palette. Selections can only be saved one MSF at a time. |
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List Selection Commands
| |
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Edit File Manually
| Allows a .csf file to be manually edited. Opens a new window, which by default uses the vi editor for editing the file. |
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Help on Commands
| Provides a list in the textport of color selection commands that can be entered from the keyboard. Each entry includes a short example. |
The Color Atoms palette contains most of the selections available for user-defined assignment of colors. Table 21 lists the selections in this palette and provides a brief functional description of each. Unlike the other palettes that affect what is displayed in the viewing area, the Color Atoms palette does not include the selections Include and Exclude. Color selections are not binary (on or off), but display and label selections are.
The Proximity Tools selection in the Color Atoms palette opens the Proximity Selections palette for assigning colors to atoms close to a portion of the structure you have selected. Any selections you make using this palette displays all proximate atoms using the current color scheme.
The selections on this palette are the same as those on the palette described in "Using proximity tools" on page 71, except that the Include and Exclude tools are not required.
Use the following exercises to become familiar with color assignment functions:
1. Make a color assignment using the pull-right menu.
Open the Draw menu and select Color Atoms to open the pull-right menu. Select By Segment. The entire peptide turns pink (color 14).
2. Make color assignments using the Color Atoms and Color Schemes and Utilities palettes.
Display the Draw menu again and select Color Atoms to open the pull-right menu. Select Selection Tools.
The Color Atoms, Color Schemes and Utilities, and Color Dials Set 1 palettes are displayed to the right of the viewing area with their default settings. The legend *Color 2* is displayed in the top- right corner of the viewing area, indicating that selected atoms will be displayed in color 2. The structure is still displayed in color 14 (pink).
3. Color the Protein backbone in PEPTIDE.msf.
Select Protein Backbone from the Color Atoms palette.
The backbone is displayed in color 2 (default = blue), and the rest of the molecule continues to be displayed in pink.
Select List Selection-Commands from the Color Schemes and Utilities palette.
The current color selection is:
DATA PEPTIDE.msf
Segm Seg1 = COL 14
PICK C N CA HA HA1 HA2 O H HN HT? OCT? OXT? CT? = COL 2
The information in red in the upper-right corner of the viewing area reads:
*Color 3*
Select Residue Type from the Color Atoms palette. A dialog box opens. From the scrolling list of residues, pick Leu. All leucine residues in the structure are displayed in red.
The current color selection is:
DATA PEPTIDE.msf
Segm Seg1 = COL 14
PICK C N CA HA HA1 HA2 O H HN HT? OCT? OXT? CT? = COL 2
TYPE LEU = COL 3
Note - you should set the bond colors to a smooth range when using this mode
Select Blue-to-Red Smooth Range from the Color Schemes and Utilities palette.
The molecule's colors and the color dials change to reflect this choice. Color 1 is blue and color 14 is red. Color numbers and charge increase in tandem.
Now select the All Atoms tool to color the whole molecule by charge.
6. Return to Molecular Modeling mode.
Select Default Colors from the Color Schemes and Utilities palette and then select Quit in the Color Atoms palette.
The application returns to Molecular Modeling mode. The peptide is displayed in pink.
From the Draw menu, reopen the Color Atoms pull-right menu and select By Element. The peptide colors return to standard element default colors.
The Property Colors command on the Draw menu gives access to functions that facilitate coloring atoms or residues according to various properties.
This opens a dialog box that sets up property coloring.
This radio button group specifies which property is to be used. The choices are:
There is a toggle box, Calculate over Residue, which can be applied to any of the first four properties. This allows the property to be computed over each residue as the Average (optionally with main/side chain discrimination), Sum, Minimum or Maximum.
If the Fourth Parameter is chosen, then there is also the choice of which item of extra information to load. This can be per-atom or per-residue information of type REAL, INT4, INT2, or ASTR.
The Position of Secondary Structure property assigns the atoms in each sheet or helical secondary structure element to consecutive color numbers, leaving other parts white. The colors should be set to a spectral ramp.
The sixth property, Residue Position, can be defined relative to each segment, each MSF or within all atoms of all loaded MSFs. Finally, you specify which of the 14 available colors to use for the property coloring and can have these automatically set up to be a Spectral or Electrostatic ramping or leave the color map as before.
Allows the property values to be normalized. The choices are:
Normalizes the values within the range 0-1, using the formula:
Normalizes the values in the range -1 to 1:
The normalization can be performed relative to all MSFs or within each MSF.
Displays a dialog box that allows the creation and adjustment of a spectral color ramp. This is a gradation of the colors through different hues, all with full saturation and intensity. The molecule is scaled down and moved so that it can still be seen to judge the effect during the adjustments, and the color legend is displayed.
The dialog box allows control over which of the 14 colors to use for the ramp. The starting and ending hues can be specified, in terms of a color wheel number or symbolic name:
RED=0 (360)
YELLOW=60
GREEN=120
CYAN=160
BLUE=240
PURPLE=270
MAGENTA=320
Intermediate hues can be specified numerically or by "thumbwheel" adjustments. You can go around the color wheel clockwise or counterclockwise: if the starting hue is red and the final color is blue, then clockwise goes through green and counterclockwise goes through purple.
Similar to Spectral Colors, but ramps from a fully saturated color down to white. There is a choice for whether the ramp should be white at the minimum color number, the maximum, or the midpoint. In the last case, two hues are specified. The typical electrostatic color scheme goes from blue to red via white.
Toggles the display of the color legend object.
By default, QUANTA uses half-bond vectors, i.e., if two atoms of different colors are bonded then the bond is drawn half one color and half the other. In some cases, in particular when coloring by a smoothly varying property, it is more visually appealing to blend the colors along the bond. This option toggles between half-bond and blended-bond style. This setting also applies to solid representations such as licorice.
In addition to the visual representation of properties as color, the values are also included in the Atom Property table.
The command PROP STAT prints information about the current property calculation to the textport. This is of the following form:
Atoms or groups of atoms can be selected and labeled. Labels include information such as atom name, residue ID, and atomic charge. Each label can be customized to contain different pieces of information. As label selections are made, labels are displayed next to the appropriate atoms. Labels can be assigned to atoms whether or not they are displayed. You can produce a labeled structure with one or more types of labels, each associated with one or more selected atoms or atom groups.
Label Atoms in the Draw menu is used to determine which atoms have labels. Labels can be displayed using the predefined choices in the Label Atoms pull-right menu or by choosing Selection Tools to open the Label Atoms and the Label Components and Utilities palettes. Using palettes requires more steps but gives you more flexibility in tailoring labels.
Selections in the pull-right menu are those used most commonly for labeling atoms and residues. See Table 22 for a list and description of the selections in this menu. Display of labels selected from the pull-right menu can be turned on and off from this menu.
Opens Label Atoms and Label Components and Utilities palettes. |
The Label Atoms and Label Components and Utilities palettes together include the same display selections as the pull-right menu, plus numerous additional choices. The Label Atoms palette selections determine which atoms or group of atoms are labeled. Table 23 lists all palette selections and provides a short functional description of each. Most of the selections in this palette work in conjunction with Include and Exclude to generate specified labels.
The Label Components and Utilities palette selections determine the information displayed in labels. Table 24 lists all palette selections and provides a short functional description of each.
Complete the following procedures for practice with generating labels.
1. Choose label information from the pull-right menu.
Display the Draw menu and select Label Atoms to open the pull-right menu. Labels are automatically turned on when you select On.
Select Atom Name from the pull-right menu. All atoms are labeled by name in bright green.
Display the Draw menu again and select Label Atoms to open the pull-right menu. Select Residue Name from the pull-right menu. The Atom Name labels are replaced by a single label per residue.
Return once more to the Draw menu and select Label Atoms. Select Off in the pull-right menu to remove all labels.
2. Choose label information from palettes.
Display the Draw menu and select Label Atoms to open the pull-right menu. Select Selection Tools from the pull-right menu to open the Label Atoms and Label Atoms Components and Utilities palettes.
Select Atom Name, Segment Name, and Show Labels from the Label Atoms Components and Utilities palette.
From the Label Atoms palette, select Include and First Atom of Residues. A dialog box asks you to choose the interval between labels on residues. Click OK to accept the default value. Labels in the format atomname_segmentname are displayed next to the first atom in each residue.
Select List Selection-Commands from the Label Components and Utilities palette.
The current label selection is:
DATA PEPTIDE.msf
FIRST =ATNAM SEGNAM
From the Label Components and Utilities palette, select Residue ID, Residue Name, and Show Labels.
From the Label Atoms palette, select Include and Alpha-Carbon Atoms. In addition to the labels on the first atom in each residue, new labels in the format residueID_residuename are displayed next to each alpha-carbon atom.
The current label selection is:
DATA PEPTIDE.msf
FIRST =ATNAM SEGNAM
PICK CA = RESID RESNAM
The selection is no longer checked and highlighted, and labels are no longer displayed. The textport message remains unchanged.
From the Label Atoms palette select Clear. All labels are removed from the screen. Select List Selections Commands.
The current label selection is:
DATA PEPTIDE.msf
4. Exit from the Label function.
Select Quit from the Label Atoms palette. The system returns to Molecular Modeling mode without saving or displaying the labels selected from the palettes.
5. Reselect labels from the pull-right menu.
From the Draw menu, select Label Atoms and open the pull-right menu. Select On. The residue labels from the first part of this exercise are redisplayed.
QUANTA uses the list of atoms contained in an MSF for all modeling operations and calculations. All the atoms in an MSF or any portion of an MSF can be selected for any particular operation or calculation and then saved to a new .msf file. Atoms that are not selected are not saved in a newly created file and are not available for computations.
In general, this facility should be used sparingly, only when it is necessary to restrict the number of atoms in memory. Use Display selections, not Active Atom selections for determining what is viewed on the screen.
The Active Atoms function provides several mechanisms, both menu- and command-driven, for specifying which atoms, groups of atoms, segments, and/or residues in active MSFs are to be used for current QUANTA modeling operations and calculations.
The Active Atoms function is located in the Edit menu. When you select Active Atoms, a pull-right menu is displayed that contains two common predefined choices for atom display: All Atoms and All Except Solvent. To select other active atom clusters, choose Selection Tools. The Active Atoms and Active Atoms Utilities palettes open on the right of the screen.
Table 25 lists the selections in these palettes and provides brief functional descriptions of each selection.
When you use the Active Atoms and Active Atoms Utilities palettes, you can make two types of atom selections: categorical and user-defined. Categorical (or automatic) atom selections specify atoms by category. User-defined (or interactive) atom selections establish specifications based on picked atoms in the display structure. You can also make a selection that allows you to enter selection commands from the keyboard.
When you have completed your selection of active atoms, unselected atoms are no longer used for any calculations. However, these atoms still exist in the MSF that you have been using, so it is possible to recover unselected atoms by selecting Include and All Atoms from the Active Atoms palette.
If you want to permanently modify the MSF, save it in a new file by using the Save As selection in the File menu. Give the new file a different name, since only selected atoms are included in the new MSF. All other atoms are deleted permanently and cannot be used again.
Use the following practice exercises to become familiar with the Active Atoms function and with the selection-command mode of making selections.
Selection commands can be entered from the command line, from the Active Atoms palette using Type in a Selection, or from the Active Atoms Utilities palette using Edit Selection Manually, which opens a shell window for editing. See Using Selection Commands on page 97 for more information about specific commands.
1. Make active atom selections using pull-right menu and palette choices.
The Active Atoms and Active Atoms Utilities palettes open. The peptide molecule changes to blue indicating that no atoms are selected. As indicated in the message in the upper-right corner of the viewing area, selected atoms are displayed in red. Red and blue are the default colors for display colors 3 and 2, respectively.
Select Residue Range from the Active Atoms palette. When the dialog box appears, fill in the data entry boxes with the residue range 1 to 15 and click OK. A portion of the molecule turns red, indicating that these atoms are selected.
The textport message indicates that 155 atoms are selected. However, the Active column of the Molecule Management table indicates that the molecule still contains 201 active atoms.
The palettes close and the molecule display changes to standard element colors. Only residues 1 through 15 are displayed. The textport message indicates that 155 atoms are selected, and the Active column in the Molecule Management table indicates that those 155 atoms are the ones that are active in the molecule. QUANTA no longer recognizes the additional atoms that were part of the original peptide.
Display the Edit menu and reselect Active Atoms to open the pull-right menu. Select All Atoms. All 201 atoms of the original peptide are restored to active status and displayed in the viewing area.
2. Make active atom selections using selection commands.
Display the Edit menu. Choose Active Atoms then Selection Tools from the pull-right menu. The Active Atoms and Active Atom Selection Utilities palettes appear to the right with their default settings.
Select Type in a Selection from the Active Atoms palette. Use the dialog box to enter commands sequentially, using the tab key or the mouse to move from line to line.
This selects the atoms (in residues 1 through 4) to be excluded from calculations
Your input is accepted and the first four residues are now displayed in color 2 (blue, unselected), with the rest of the molecule displayed in color 3 (red, selected).
This message is displayed in the textport as the commands are entered:
Select Finish from the Active Atoms palette. The molecular display returns to standard mode, and the modified structure becomes a new .asf file that will be incorporated into the .cst file to be used for calculations.
3. Save the modified structure in a new MSF
Display the File menu and select Save As. A dialog box containing options for saving a structure is displayed.
Write out current connectivity
Apply rotational transformations
The File Librarian is displayed, prompting for the new file name. Enter the name newpeptide.msf and select the SAVE button.
The number of atoms contained in the structure remains at 164. The following message is displayed in the textport:
164 atoms selected for molecular structure newpeptide.msf
164 atoms will be displayed
Since the changed MSF is saved in a new file, the content of the original MSF, PEPTIDE.msf, is not changed.
QUANTA generates selection commands every time you change any aspect of the way a molecular structure is displayed or used in calculations. You can enter selection commands directly from the keyboard as an alternative to making selections from menus or palettes or in combination with such selections. When you become familiar with selection commands, keyboard entry can provide a quicker, more accurate method for making complicated selections.
Atom specifications used in selection-commands take the basic form: atomname segmentname: resid filename.msf.
Selection-commands can be combined within a command line using the logical operators .and., .or., .not., and .xor. For example:
> type try phe .and. round cb 38
selects the atoms contained in any aromatic residue around the beta carbon in residue number 38.
Wildcards can also be used with appropriate selection-commands, including type, pick, atom, and at.Table 26 lists the wildcards that are available and describes the way each operates.
For example, to pick all protons attached to the beta carbon in a protein, type the selection-command:
> Pick HB+
To match all name carbons with three characters in their names, type the selection-command:
> Pick C%%
can be used with the commands x/y/zcor, fourth, and charge to specify ranges of values. For example:
> four gt 10
selects all atoms for which the currently loaded fourth parameter value is greater than 10.
Table 27 lists commands that can be used interactively with the Display Atoms, Color Atoms, Label Atoms, and Active Atoms menu selections. These commands can be entered from the command line, from a dialog box that opens when you choose Type in a Selection, or from a shell window that opens after you select Edit Selection Manually in the appropriate palettes. The commands are listed alphabetically.
You can customize the default display and coloring regime to be used when an MSF is first created or opened. This can be done by creating files named default.dsd and default.csd, respectively, containing the desired selection commands. For display selections, this can be done using the function Default Display Mask on the Preferences menu. The definition of solvent can be overridden by a file, solvent.asd, containing a suitable selection command. The definitions of what constitute protein or nucleic acid main and sidechains can be redefined by creating a set of files named backbone_prot.asd, backbone_nucl.asd, sidechain_prot.asd, and sidechain_nucl.asd. These should contain just atom names, with wildcards if desired, since they will be assumed to be PICK selections.
The above files are all optional. They are looked for first in the current directory, and then in a directory pointed to by the environment variable $QNT_USR if you have set this up. If the file does not exist then the normal defaults are used.
In QUANTA, you can customize many aspects of MSF display as well as select and modify the atoms involved in modeling operations and calculations. This chapter deals with both types of manipulation.
Operations for customizing displays are carried out by the Display Atoms, Color Atoms, and Label Atoms functions in the Draw menu using pull-right menus and palette selections. Keyboard commands can be used interactively with these functions. Customization of atom display, colors, and labels is superficial, never affecting basic structural information used in modeling operations and calculations. The power of the display manipulations lies in their ability to focus attention on certain aspects or areas of a single molecule or several molecules.
The Active Atoms function in the Edit menu affects the atoms of an MSF used in modeling operations and calculations. All or any portion of the atoms in an MSF can be selected for any particular operation or calculation and then saved to a new .msf file. Atoms that are not selected are not saved in the newly created file.
Although the selection mechanisms for the Display function are similar to those of the Active Atoms function and MSF displays may look the same, the Active Atoms function is fundamentally different from the display function. Don't confuse the two functions. Using them interchangeably may lead to a loss of data.
