The Sequence Viewer window comes up automatically upon entering Protein Design, Protein MODELER, Protein Health or Protein Profile Analysis and closes when exiting these applications. The window can be iconized or expanded by clicking the appropriate icons in the top right of the frame of the window.
Sequences, for which the only information is the amino acid sequence, are supported and can be read in using the utilities in the Sequence Data option under the Files pulldown. Sequences can be converted to MSFs using the tool in the Protein Editor utility.
While the program is running, a file called protein_default.aln (which is in an extension of Clustal format) is kept up to date with the current sequence selection and alignment. On exiting QUANTA, this file is written to the constants file, .cst, to be saved until the next session.
By default, Protein Design handles up to 30 sequences and 50,000 residues in all the sequences. There is also a limit of 2000 columns in the sequence viewer. These values can be reset by typing the command SEQM into the command line. You will get a dialog box in which you can enter the required maximum dimensions. These values will be saved and used in future QUANTA sessions.
In general, clicking any item on the Sequence Viewer is done with the left mouse button except for those operations which drag either a sequence or slider and these use the middle mouse button.
The main area of the Sequence Viewer displays the sequences of all the selected MSFs which are recognized as proteins and the selected sequences. Sequences can be read into QUANTA using the Read Sequence/Alignment File option on the Sequences pull-right under the Files pulldown (as described in Chapter 2.). By default, the MSF sequences are displayed above the non-MSF sequences. The residues from MSFs are colored the same as the Ca atom of that residue in the molecule window and the sequence residues are colored according to one of the sequence coloring schemes, by default according to an hydrophilicity classification.
When you pick any residue, its ID is reported to the textport, and, if Highlighting is on (See section below on icon functions) and the residue is in an MSF, then the sequence residue will be highlighted by a yellow box and the Ca atom on the molecule will be highlighted with a yellow star.
Picking the residue in the sequence can be used for selection in many other situations. For example, to focus on a particular area of the molecule, choose the Set Origin tool from the Protein Utilities palette and then pick a residue on the Sequence Viewer. The Ca atom of the picked residue will be set in the middle of the molecule viewing area.
The viewing area can be adjusted using the red slider bars below and to the left of the main viewing area. To move the slider, hold down the middle mouse button with the pointer over the slider and then drag in the required direction. To change the scale of the viewing area, hold down the shift key and the MIDDLE mouse button with the pointer over the slider bar. The dragging up/down or left/right will expand or contract the slider bar and the scale of the main viewing area.
The names of the MSFs or sequences appear to the left of the main viewing area. Clicking a sequence name toggles sequence activity off and on. The names of inactive sequences are colored grey. If the sequence corresponds to an MSF, the MSF activity, as shown in the Molecule Management Table, will also be updated. The sequence activity can also be updated using the Activity button to the lower left (labeled A).
The residue IDs for every tenth residue are shown beneath the main viewing area. By default, these are the IDs for the first sequence in the table. The name of the sequence whose IDs are displayed is to the left of the IDs. Picking this sequence name will bring up a dialog box to enable selection of an alternative sequence to be labeled. The residue interval of the labels and whether to include segment names in the IDs can be changed from the Options button to the lower left (labeled O).
Several applications automatically draw graphs to the Sequence Viewer. The Protein Design Secondary Structure Prediction module has options to plot Hydrophobicity, Conservation and Composition. These analyses are applied only to the currently active sequences and multiple plots may appear overlaid (e.g., the hydrophobicity of all active sequences will be generated by the Hydrophobicity tool).
Each plot is a different color and the legend to the left of the graph gives the name of the sequence or the parameter plotted in the appropriate color. Picking the plot name in the legend will toggle off and on the display of the plot. The legend for plots not currently displayed are colored grey. For some types of plots, the legend also includes a Difference option. When this is picked, the difference of two currently displayed plots will be shown. If there are more than two currently displayed plots, the difference will be between the first two.
The plots are drawn with the parameter corresponding to a particular residue or column in the sequence alignment above the appropriate residue or column. If the sequence alignment includes gaps then there will be gaps in the graph plots for that sequence. When the tools in the Align and Superpose module are used to change the sequence alignment, then the graph plots will be automatically updated to keep in register with the sequences. If a difference plot is displayed then it will be updated with the alignment.
Toggles on/off the cross highlighting of the residues in the Sequence Viewer and molecule window. If the tool is off, then the icon is colored grey. When the cross highlighting is on then picking either a residue of an MSF sequence in the Sequence Viewer or any atom of a residue in the molecule window will highlight the Sequence Viewer residue with a yellow box and the Ca atom of the molecule with a yellow star.
Picking this icon brings up a dialog box with options to control the appearance of the Sequence Viewer. The heights of sequence and graph viewing area can be set - the size of the sequence viewing area is proportional to the number of sequences currently displayed up to some maximum number of sequences above which the height of the viewing area is constant. The interval of the sequence residue ID labeling can be changed from the default of ten residues and the inclusion of the segment ID in the label can be toggled off. The match symbol, a vertical yellow bar, is used in the Align and Superpose module to denote the homologous regions of sequence. The thickness and color of this annotation can be changed. The highlight annotation is a pale yellow box around a residue in the sequence viewer which indicates a residue selected while the Highlight option is on. The thickness and color of this annotation can be changed.
The residue interval of the sequence labeling can be changed and the inclusion of segment IDs in the label can be toggled on or off.
This icon only becomes available after a graph has been drawn in the Sequence Viewer. Picking this icon will toggle off or on the display of the graphs and will contract the size of the Sequence Viewer window when the graph is toggled off. The same graph will be restored when it is toggled on.
After picking this tool, you should pick a residue on the Sequence Viewer or a molecule and the focus of the Sequence Viewer will be changed to place that residue at the center.
Expand the Sequence Viewer display to show the full sequences.
The activity of any individual sequence can be toggled by picking the name of that sequence on the viewer. To change the activity of several sequences you may find it more efficient to use the selection dialog box brought up by this icon.
This icon brings up a dialog box in which you can select which sequences are displayed on the viewer and the order in which they are displayed. Any currently undisplayed sequences are listed in the left hand box entitled Hide in the order that they were read into QUANTA. The right-hand box entitled Display in Order lists all currently displayed sequences in the order in which they are displayed.
If a sequence is selected from the Hide list, it will be moved to the bottom of the Display list. If a sequence is selected from the Display list, it is moved to its appropriate place in the Hide list. The Hide All and Display All buttons will move all sequences to the appropriate list. It is possible to insert a sequence into the display list at a specified position by clicking the Insert Above button and then clicking the sequence above which the insertions should take place. The symbol ->->->...? will appear in the Display list and any sequence picked from either the Hide or Display list will move to that position. The Insert Above tool is switched off by clicking the Hide button.
The user is prompted to enter a short amino acid sequence and the first occurrence of this short sequence in an active sequence will be highlighted by a red box in the Sequence Viewer. The icon is changed to ... and when picked again will find the next occurrence of the sequence unless there are no more occurrences, in which case it will revert to ? and remove display of the highlight box.