standard increments, template-based, antibody CDRs
Renumber Residues Dialog Box
Renumber the residues in one or more sequences, either by simple incrementing of the number or by copying the numbering from a template.
To open this dialog box, choose Renumber Residues from the Edit menu in the Multiple Sequence Viewer/Editor Panel.
- Using
- Features
- Additional Resources
Using the Renumber Residues Dialog Box
The simple renumbering scheme can be applied to one or more sequences selected in the sequence viewer. The residue at the first (ruler) position in the sequence viewer is assigned the value in the First position text box, then the next residue number is this value plus the increment, and so on. You can preserve the value of the insertion code for residues that have them, but the residue numbering is incremented regardless of the insertion codes.
One use of the simple renumbering scheme is to perform an alignment of several sequences, and then renumber the sequences with the simple numbering scheme. This makes it easy to select the same part of the alignment in any of the sequences by using the residue numbers.
You can also copy the residue numbers of an aligned template to a sequence, in the Template-based tab. Insertions in the sequence (template gaps) are not renumbered, but retain their original numbers.
When you click OK, a confirmation dialog is displayed if multiple sequences with associated structures are renumbered.
Renumber Residues Dialog Box Features
- Method options
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Choose the method for renumbering the residues. The tools displayed below depend on the choice of the method.
- Standard increments method
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Renumber the sequence in a uniformly increasing sequence.
- Starting number text box
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Specify the residue number for the first residue in the renumbered sequence or set of sequences, if multiple sequences are selected. This value is applied to the leftmost residue of all the selected sequences.
- Increment text box
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Specify the increment to add for each residue. You might want to have a larger increment if you intend to add residues and want to avoid using insertion codes.
- Preserve insertion codes option
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Keep the insertion codes from the input sequences. The residues that have the same number but different insertion codes now have different (sequential) numbers but keep the insertion codes. For example, 15A 15B 15C 15D might be changed to 22A 23B 24C 25D.
- Template-based method
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Import sequences to be used as templates for renumbering the sequence that is selected in the sequence viewer. The template is aligned to the sequence, and the residue numbers for the template are copied to the sequence, with addition of insertion codes if necessary. Residue numbers for insertions in the sequence are not changed, so this feature is most useful when the template and the sequence are very similar.
- Choose Template button
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Choose a template PDB structure for the residue renumbering. Opens a file selector so you can select the file containing the structure. The PDB ID is reported to the right of the button, and the table below is filled in with the residue numbers, insertion codes and names.
- Template residue table
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Shows the residue number, the insertion code, and the residue name for the chosen template.
- Antibody CDRs method
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Renumber an antibody according to a chosen scheme for the CDRs.
- Numbering scheme option menu
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Choose the numbering scheme to use, from Chothia, Enhanced Chothia, Kabat, IMGT, AHo. The default is the scheme in use prior to renumbering. If any sequence does not have antibody annotations, they are added before renumbering, with the default Kabat scheme.
- CDR numbering table
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This table shows the numbering for the CDR loops for each sequence, with the start and end residue and the length for each loop.