João Rodrigues wrote: > When MODELLER creates a new model, it renumbers it. The first residue is > 1, second is 2, etc.
Indeed, because that's the only way you can reliably number the model. You can't use the template numbering - what would you do if you had an insertion in the model, or you had multiple templates that had different numbering?
> How can I force these residues to obey the original template numbering? > Say, if the template starts at residue 54, MODELLER's models will start > with 54?
1. You can use the res_num_from() method to copy residue numbers and chain IDs from another model: http://salilab.org/modeller/9v7/manual/node176.html
2. You can use the rename_segments() method to change the chain ID and starting residue number for each chain: http://salilab.org/modeller/9v7/manual/node177.html
3. You can change the number of a given single residue by assigning directly to Residue.num: http://salilab.org/modeller/9v7/manual/node322.html
You can use any of these approaches in combination with the automodel class by overriding either the user_after_single_model method (http://salilab.org/modeller/9v7/manual/node67.html) or the special_patches method (http://salilab.org/modeller/9v7/manual/node66.html). The difference is that the second method changes the residue numbers *before* any restraints are generated, so if you add your own restraints, select residues, etc. you should use your new numbering. user_after_single_model happens immediately before the generated model is written to a PDB file, so any selection of residues would still use the regular Modeller "starts at 1" residue numbering in this case.
Ben Webb, Modeller Caretaker