Thanks very much this is really helpful and has solved my problem.

 

From: Modeller Caretaker <modeller-care@salilab.org>
Date: Monday, October 16, 2023 at 7:36 PM
To: Isabel Elliott <I.G.Elliott@soton.ac.uk>, Isabel Elliott via modeller_usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] Missing residues - restrain crystal coordinates

CAUTION: This e-mail originated outside the University of Southampton.

On 10/16/23 8:15 AM, Isabel Elliott via modeller_usage wrote:
> I am trying to model missing residues into my crystal structure
> following the method on the website:
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.org%2Fmodeller%2Fwiki%2FMissing_residues&data=05%7C01%7CI.G.Elliott%40soton.ac.uk%7C5a8a05950f774990fea508dbce76d646%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638330782026794015%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ve2YK2AHvM9JVD%2BF%2Fvb7Ywz62oJJLJ5cd6bdoE4uUgQ%3D&reserved=0. I am also trying
> to restrain the crystal coordinates so that only missing residues move
> (and the rest of the original crystal coordinates remain the same)
> during refinement using the select_atoms method. However when I compare
> my final models produced by my script to my original crystal structure,
> I find that the side chains of several amino acids three of four amino
> acids away from the missing residues have been flipped. How can I ensure
> that only the missing residues are refined and the crystal coordinates
> remain the same? I am wondering if Ive missed something important out
> of my script. See my script below.

In your script you have defined the select_loop_atoms method, *not*
select_atoms. The script is essentially doing three things:

1. Building an initial model, using your template where the sequence is
the same, and internal coordinates where you have gaps or sequence
differences. This file is generated in PDB format with a '.ini' extension.

2. Refining a subset of the model atoms, defined by select_atoms (by
default all atoms will be refined).

3. Further refinement using Modeller's loop modeling protocol,
potentially of a different subset (defined by select_loop_atoms).

If your template is missing some sidechains then they will be filled in
in step (1) above - and you'll see that in the .ini file. Otherwise,
defining select_atoms, as described in the wiki page at
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.org%2Fmodeller%2Fwiki%2FMissing_residues&data=05%7C01%7CI.G.Elliott%40soton.ac.uk%7C5a8a05950f774990fea508dbce76d646%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638330782026794015%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ve2YK2AHvM9JVD%2BF%2Fvb7Ywz62oJJLJ5cd6bdoE4uUgQ%3D&reserved=0, is what you need.

        Ben Webb, Modeller Caretaker
--
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