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Prime Structure Prediction Menu Bar |
The Prime Structure Prediction menu bar contains four menus, File, Edit, Display, and Step. Some of the options in these menus are also available as toolbar buttons.
The File menu contains commands for creating, naming, opening, and deleting Prime runs. (Also see Using Prime Runs.) The other menu options are Export Sequences and the Job Options command, which allows you to designate a host machine and a user name for each type of Prime job.
The run commands are:
Create a new run. You are asked for a name (all names must be unique.) Prime starts the new run at the first step.
Save the current state and provide a new run name. Prime leaves the existing run and switches to an identical run with the new run name.
Specify a new name for the current run. If the run name is not unique, a warning message appears.
Delete the current run. You will be asked for confirmation.
View a list of options for switching to another run. The list includes the four most recently used runs. If there are more than four runs in the current project, click the More option and select the run you want to open from the dialog box.
The other options are:
Click to open the Export Sequences panel. All sequences (including secondary structure assignments and predictions) currently visible in the Sequence Viewer will be exported to a single file in native Maestro format. If HMMER/Pfam, ssa, or ssp data is currently hidden under the parent sequence it describes, only the parent sequence is exported.
Click this option to open the Job Options panel, which is described in the Prime Job Options topic.
The Edit menu contains commands for editing sequences and secondary structure predictions. These editing tools are also available as buttons on the Prime toolbar, and are described in the Prime Toolbar topic:
Select
Crop
Edit SSP
Set Template Regions
Slide Freely
Slide As Block
Add Anchors
Lock Gaps
Unlock Gaps
The Display menu contains the following options governing the visualization of structures and sequences. Color schemes are described briefly here; use the Legend command in this menu to view the assignment of each color and symbol used in each color scheme and sequence representation.
This command opens a menu of coloring options. In Prime-SP, only one color scheme can be used at any given time. Each step in Prime has an appropriate default color scheme. You may choose a different scheme using this menu. When an amino acid sequence is added to the Sequence Viewer, it is colored according to the scheme that is currently selected.
When the structure associated with a sequence is displayed in the Workspace, it is generally colored using the same scheme as the sequence. However, protein structures in the Workspace are sometimes colored using other color schemes:
When a PDB structure is imported, it is displayed in the Workspace using a Maestro error reporting color scheme in which complete recognized residues are gray, incomplete residues are red, unknown/nonstandard residues are orange, residues with multiple location indicators are green, and recognized residues with some unrecognized atoms are blue. See the PDB Conversion topic section on Color-Based Error Reporting for more information.
At the end of the Prime workflow, when an output structure is added to the Project table, it is colored to represent the quality of the model. The final structural analysis provides information about potential problems: clashes, bad bond lengths, and bad bond angles. Each atom in the structure is assigned a color, from blue (no problems) through gray to red (at least one severe problem). (This analysis can be viewed by using the Protein Reports panel.)
The Prime color schemes are:
All sequences are colored standard gray.
The query sequence is colored standard gray. Each of the other sequences uses a different color.
Each amino acid sequence is colored according to the array of residue type colors.
Each amino acid sequence is colored according to the array of residue property colors (fewer colors than residue type).
The query and templates are colored in a pairwise manner. Matching residues are colored according to their residue type, and non-matching residues are colored standard gray. If more than one template is chosen, the query will have more colored residues because the effect is cumulative. When only the query sequence is shown, it is colored standard gray for all residues.
Aligned query and template residues that are identical (highly conserved) are colored red. Aligned query and template residues that are similar according to the BLOSUM62 scoring matrix (conserved) are colored yellow. Gray is used for residues with no homology.
The query sequence, which has no secondary structure assignment (SSA), is colored standard gray. All other amino acid sequences should have SSAs. Secondary structure assignments are displayed as a linear series of red cylinders (alpha helices), cyan arrows (beta strands), and gray line segments (loops/random coils.) This option applies the same color scheme to the amino acid sequences that have SSAs, and to the model in the Workspace.
Only available for the Comparative Modeling path, when a model is being built (in Build Structure) or refined (in Refine Structure). Before a structure is built, the query sequence is colored standard gray. Afterward, both the query sequence and the predicted structure are colored according to template ID for each region (using a cycle of assigned colors). Each template sequence is colored with its assigned color, but only in the region used to build the model. The unused portion of the template is colored dark gray.
At any step in which the Sequence Viewer is displaying sequences that have associated structure (all steps except Input Sequence), color by proximity mode is available. When you select this color scheme, the current sequence colors do not change immediately. Instead, when the mouse is over a sequence that has structure, the cursor changes to indicate that proximity can be calculated. You can then select one or more contiguous residues in the sequence, and the system will color that sequence based on the proximity to the selected residues. No other sequences will have modified colors (even if they have structure too and are in proximity of the selected sequence). Proximity is calculated based on the shortest distance between any two atoms in two residues, not including the bonded C and N atoms in the residues next to the selected residues.
To change the proximity cutoff, select Preferences from the Display menu and change the number in the Proximity cutoff text box.
The font size of letters and numbers in the Sequence Viewer can be changed by choosing a point size from this submenu. The default size is 10 points.
The options for showing structures in the Maestro Workspace include:
This option controls whether secondary structure assignments are shown in the Sequence Viewer.
This option controls whether the PFAM annotation shows only the highly conserved residues, or shows other family annotations as well. In the full annotation, capital letters indicate highly conserved residues, lowercase letters indicate a match to the HMM, + means the match is conservative, and a blank indicates that the residue does not match the HMM.
This option opens the Sequence Viewer Legend panel, which allows you to view the assignment of each color and symbol used in each color scheme and sequence representation. It is also available when you right-click on a sequence in the Sequence Viewer.
Select this option to open the Proximity dialog box. The value entered in this text box defines the proximity cutoff for the Proximity color scheme. The default is 4.00 Å.
The Step menu provides another way to navigate between steps in Prime. It includes the following options:
When this check box is selected, the Prime Guide is displayed (the default). Deselect the check box to hide the Guide.
Click this option to go to the Input Sequence step.
Click this option to go to the Find Homologs step.
There is an option to click to go to each step in Prime-SP. A red diamond is displayed next to the option to go to the current step. Options to go to steps that are not available appear dimmed.
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