On Mon, Oct 26, 2009 at 1:48 PM, Modeller Caretaker <modeller-care@salilab.org> wrote:

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
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