Re: [modeller_usage] Modelling in/dels and residue substitutions
To: Jared Slosberg <>, "" <>
Subject: Re: [modeller_usage] Modelling in/dels and residue substitutions
From: Modeller Caretaker <>
Date: Tue, 12 Nov 2019 12:57:58 -0800
On 11/11/19 1:55 PM, Jared Slosberg wrote:
I am interested in creating models for variants of a protein with a
known cryo-EM structure. My approach for the substitutions is to use
the mutate_model script. However, I would also like to model predicted
changes in structure to nearby residues. I altered the script in this
way in an attempt to optimize over a range of residues, but I saw no
difference in the resulting model than with only the one residue selected.
s =
selection(mdl1.chains[chain].residues[start],mdl1.chains[chain].residues[stop])
This will select the start residue and the stop residue, not the
residues in between, which is probably not what you meant to do.
residue_range() is probably what you want here:
However, this has obviously left the ends of the aligned sections fixed
in space, so that the region that I want to fold "freely" is fixed at
these two points. This results in them "stretching out" rather than
being able to fold as I would like. I hope that I am being clear. Is
there better method to create variants with insertions that is more
flexible?
If you don't want the ends fixed, unalign a longer segment. If you do
want them fixed but want better conformational sampling, this is
precisely what loop modeling is designed for: