Re: [modeller_usage] Stop renumbering of new model

[Modeller Caretaker <>]

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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