Re: [modeller_usage] Mutate and refine residue placement
To: Steve Seibold <>
Subject: Re: [modeller_usage] Mutate and refine residue placement
From: Modeller Caretaker <>
Date: Wed, 18 Nov 2009 12:11:32 -0800
On 11/18/2009 05:46 AM, Steve Seibold wrote:
Having successfully install the newest version of Modeller on my new
machine (I ran some test cases), I would like to attempt the
construction of a mutant of my protein using the tutorial:
http://salilab.org/modeller/wiki/Mutate%20model. However, my protein has
metal and DNA with it and, so, I am not sure how Modeller will deal with
this. Can you inform me? I am worried that Modeller will simple fail
with the error that it can not recognize certain atoms. If it does, is
there away I can get around this? Could I do only a local (around the
mutated site) minimization only, ignoring the rest of the protein?
The easiest way to find out is to run it and see. ;) No, it won't have
any problem with any HETATM residues in your protein (as long as you
don't try to mutate those residues, of course). Just as for regular
homology modeling, the HETATM residues will be simply copied from input
model to output.
As for "local minimization", that's exactly what that script does. Only
the residue you mutate is moved - every other residue in the protein
remains fixed. You can, of course, change the script if you want to do
something different - e.g. to allow nearby residues to move as well.