Adjust Residue Numbering Panel
Renumber residues in one or more proteins based on a mapping derived from structural alignment to a template structure.
To open this panel: click the Tasks button and browse to Workspace Operations → Adjust Residue Numbering.
- Using
- Features
- Additional Resources
Using the Adjust Residue Numbering Panel
This script renumbers residues based on an SKA structural alignment, which generates a mapping of the residues in each aligned structure to the reference structure (the first structure). In reference mode, all residues are assigned numbers using the numbering of the first structure, with proper allowance for gaps and differing sequence lengths. In alignment mode, all structures are renumbered based on the residue positions in the alignment, with the first residue in the first structure assigned the number 1.
This script changes non-standard amino-acid types to standard ones for SKA compatibility e.g. HIE, HID, HIP to HIS, and CYX to CYS. 'alignment' mode is limited to 52 input structures and the renumbering is very dependent on the sequences used (i.e. count, their length etc.).
Adjust Residue Numbering Panel Features
- Use structures from option menu
- Open Project Table button
- File name text box and Browse button
- Calculation mode options
- Change coordinates (superimpose) option
- Job toolbar
- Status bar
- Use structures from option menu
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Choose the structure source for renumbering.
- Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item.
- File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
- Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item.
- Open Project Table button
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Open the Project Table panel, so you can
- File name text box and Browse button
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Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.
- Calculation mode options
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Choose the method by which the sequences are renumbered. The renumbering makes proper allowance for gaps, insertions, and differing sequence lengths.
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Reference—Set the residue numbers so that they are the same as in the reference structure (the first structure in the set of source structures), making use of the mapping derived from the structural alignment. This means that each residue in each structure is assigned the same residue number as the residue to which it is mapped in the reference structure.
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Alignment—Set the residue numbers based on the mapping from the alignment, starting from 1 for the first residue in the reference (first) structure. The numbering continues according to the alignment, taking account of gaps and insertions. If the first residue in the first structure maps to a residue in another structure that is not the first residue, the preceding residues in this other structure are given negative residue numbers.
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- Change coordinates (superimpose) option
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Replace the coordinates of the output structures with those from the structural alignment. By default the output structures retain the coordinates of the input structures.
- Job toolbar
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Manage job submission and settings. See Job Toolbar for a description of this toolbar.
The Job Settings button opens the Adjust Residue Numbering - Job Settings Dialog Box, where you can make settings for running the job.
- Status bar
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The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.
Use the Reset button
to reset the panel to its default settings and clear any data from the panel. The status bar also contains the Help button
, which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a 
button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.