Insertions, Deletions, and Loop Swaps Panel
In this panel you can specify a residue to be inserted or deleted, or you can define a string of residues to be modified in a loop swap. Because insertions or deletions require additional refinement of the residues around the modification site, all modifications made by this panel require a loop swap calculation.
To open this panel, click the Tasks button and browse to Biologics → Residue and Loop Mutation.
- Using
- Features
- Additional Resources
Using the Insertions, Deletions, and Loop Swaps Panel
The basic workflow is as follows:
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Choose the loop to be modified.
For best results select at least two residues on either side of the residues to be modified. The selection can be made either by using the sequence viewer or by selecting residues in the Workspace.
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Click the Workspace Selection button to load the original loop into the table.
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If desired, load a new structure and select residues to specify a starting set of residues for the replacement loop.
By default, the replacement loop starts out identical to the original loop.
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If desired, edit the replacement loop by clicking on residues in the table and specifying an insertion, deletion or mutation at that point.
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Click Accept to return to the Residue and Loop Mutation panel with the loop swap defined.
Selecting the loop in the Workspace allows you to visually identify the loop. To ensure that you are picking residues in the Workspace to define the loop, set the selection scope to Residues (see Selecting Atoms by Picking in the Workspace). You can then pick residues that belong to the loop you are interested in. The residues that you pick are highlighted in the Workspace (yellow dots) and in the sequence viewer (white letter on blue background).
Selecting the loop in the sequence viewer allows you to easily search for patterns in the sequence, or to use the secondary structure assignment (SSA) to identify loops. The SSA has no annotation where there are loops (the absence of any other secondary structure). To search for patterns in the sequence, enter the pattern in the Find Pattern text box, with a dash separating each residue from the next, e.g. D-A-P. The syntax is summarized in the tool tip for the text box, and is given in more detail in PROSITE, syntax, patterns, reactive residues, motif, motifs. You can use the arrow keys to step through the patterns. All of the matches are selected in the Workspace, so you might have to select the loop that you want in the Workspace, or by clearing the Find Pattern text box, then selecting the residues to use.
You might want to align the sequence for the replacement to the sequence for the original structure, so that you can select the loop by its alignment. To do the alignment, make sure that the original sequence is at the top of the sequence viewer (use the shortcut menu for the sequence name to move it if necessary), and add the replacement sequence to the selected sequences. You can then use either the pairwise alignment tool or the multiple alignment tool to align the sequences (using ClustalW).
You can also do manual alignment, with locking and unlocking of gaps. See the Multiple Sequence Viewer/Editor Panel document for more information on doing manual alignment.
Insertions, Deletions, and Loop Swaps Panel Features
- Sequence viewer and tools
- Original loop section
- Replacement loop section
- Replacements table
- Number of models to generate box
- Loop prediction options
- Accept button
- Sequence viewer and tools
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The sequence viewer can be used to import a structure from a number of sources, perform sequence alignment of imported structures, and specify a string of residues to define a loop. You can use any sequence in the sequence viewer to define the original loop or the replacement loop. The sequence viewer consists of an upper toolbar, a sequence display area, and a lower toolbar for alignment tasks.
- Upper toolbar
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This toolbar has tools for importing sequences, undoing and redoing sequence editing, and finding patterns in a sequence.
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Import button—Import sequences into the sequence viewer. The choices are:
- Browse for File—Open a file browser in which you can navigate to the desired location and select the file that contains the sequence. The allowed file types are Maestro and PDB.
- From PDB ID—Import the sequence from the specified PDB ID. Opens the Enter PDB ID dialog box, in which you can enter the PDB ID of the sequence. The sequence is retrieved from a local copy of the PDB if it is available, or from the RCSB web site, depending on the preference set for PDB retrieval.
- From Workspace—Import the sequence for the structure that is displayed in the Workspace.
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Undo and Redo buttons—Undo or redo the actions taken in the sequence viewer.
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Arrow buttons—These buttons can be used to step through instances of the pattern, in the forward or reverse direction.
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- Sequence display area
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The sequence display area shows the sequence of the Workspace structure and any sequences that you import. You can drag over multiple residues to select them. Each pane of the sequence display area has a shortcut menu that allows you to perform some actions on the sequence for display or selection.
- Alignment toolbar
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This toolbar allows you to perform tasks related to sequence alignment, which can be done manually or automatically.
Lock gaps
Lock gaps in the sequences so that they are not filled when performing manual alignment. The locking is applied once. Gaps created after locking is done are not automatically locked. To lock them, click this button again. Locked gaps are indicated by a dash (-); unlocked gaps are indicated by a tilde (~). If you have a residue selection, gaps are only locked in the selected region.
Unlock gaps
Unlock gaps in the sequences after they have been locked. This allows gaps to be filled when performing manual alignment.
Pairwise Alignment
Align the selected sequences with the query sequence one at a time (pairwise), using ClustalW.
Multiple Alignment
Align the selected sequences simultaneously, using ClustalW. The sequence alignment is restricted to the selected columns in the sequence viewer.
- Original loop section
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Click this button to use the current Workspace selection as the original loop to be modified.
Replacement of loops require 1 or 2 stem residues on either side of the modified residues to also be considered as part of the loop in order to properly fit the new loop onto the structure. For best results, it is recommended to include these residues on the original loop specification. For example, if a single residue is being deleted, the original loop should consist of five residues - the residue to delete and the two residues on either side of it.
- Replacement loop section
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By default, the replacement loop starts with the same residues as the original loop. Use the Workspace Selection button to select a different set of residues as the starting point for the replacement loop, or use the Set to Original Loop button to reset the replacement loop and begin again. You can display a different protein in the Workspace and select the loop from that protein.
- Replacements table
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This table is used to modify the replacement loop residues to create the new loop that will replace the original loop. Clicking on a table cell opens a menu that allows you to delete or mutate the current residue or insert a new residue before or after the current residue. The change is applied to the Replacement row, regardless of which cell you click on at a given residue position. The Insert Before, Insert After, and Mutate items display a list of 20 standard amino acid residues that you can select.
When you choose to insert a residue, a new column is added to the table before or after the current position. The cell in the Original row has three dashes, to indicate that there is no residue in the sequence at this position. The cell in the Replacement row has the residue name between two colons, to indicate that the chain and residue number are not yet assigned. Insertion codes are added for the inserted residues when the job is run.
If you delete a residue, the cell in the Replacement row is set to three dashes, to indicate the deletion. Likewise, if you mutate a residue, the cell in the Replacement row has the new residue name between two colons.
- Number of models to generate box
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Specify the number of new structures to be returned with the replacement loop swapped for the original loop. Different models may have different loop geometries.
- Loop prediction options
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Choose whether to create the loops via a fast table-lookup method or via a full Prime loop prediction. No additional refinement beyond these methods is done for new loop predictions.
- Accept button
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Click this button to return to the main Residue and Loop Mutation Panel. Click the Mutate button on that panel to begin the loop swap calculation.