Re: [modeller_usage] Stop renumbering of new model
To: João Rodrigues <>
Subject: Re: [modeller_usage] Stop renumbering of new model
From: Modeller Caretaker <>
Date: Mon, 26 Oct 2009 13:48:42 -0700
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
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
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
(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.