Re: [modeller_usage] keeping original residue numbers in final model
To: Mauricio Carrillo Tripp <>
Subject: Re: [modeller_usage] keeping original residue numbers in final model
From: Modeller Caretaker <>
Date: Tue, 11 Nov 2008 18:49:02 -0800
Mauricio Carrillo Tripp wrote:
> Is there a way to keep the original target's residue numbering in
> the final model instead of having them sequentially numbered
> starting at 1?
Sure, but it depends on what you're doing... Are you using automodel? If
so, what is your alignment? Or are you building your model in some other
If you have a PDB file containing the original residue numbering, you
could use res_num_from(). See
Alternatively, you can write a little loop in Python to go through all
the residues in your model and assign new residue numbers and/or chain
IDs (each residue object has a 'num' member, which is the PDB-style
residue number). This gives you much more flexibility.
If you're using automodel, these modifications could go in
special_patches (in which case you'll also need to use your new residue
numbers in any extra restraints you add) or in user_after_single_model.
> As an example, this is my target's sequence (NOTE: "-" are not
> gaps, are missing/unknown residues):
If you're using automodel to build a model with intentionally missing
regions, you need a chain break (/) rather than/as well as gaps for each
region. Otherwise, there will be no break in the backbone, which is
probably not what you want.
> SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00
If this is really a sequence, all the fields after SEQUENCE: itself are
ignored anyway, so it's best to leave them blank to avoid confusion. If
this is actually a structure you should say structureX: rather than
SEQUENCE: and name the PDB file containing the structure that matches
your sequence (not an alignment file, as you appear to be doing).
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage