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Re: [modeller_usage] Stop renumbering of new model



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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