[Chimera-users] Editing sequences within Chimera

[Gregory Babbitt]

I am not sure if anyone else does this, but sometimes I will use swapaa to change rotamer(s), then go to MD/ensemble analysis and run just the dock/structure prep (i.e. add H) and then energy minimization tab under 'molecular dynamic simulation'. I usually increase the default values to several thousand steps of steepest descent.  If you check the options box for 'live run' you can watch the structure morphing and stabilizing..then resave as new PDB file.

Anybody have any thoughts as to if this is a reasonable combination of steps in Chimera?

Greg at RIT

________________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, July 26, 2019 10:54 AM
To: Joshua Plank
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Editing sequences within Chimera

Hi Josh,
I guess you mean actually changing the 3D structure.  Yes, you can “swap” amino acids by replacing side chains with the Rotamers tool (menu: Tools.. Structure Editing… Rotamers) or the “swapaa” command.  This only does a simple replacement; it does not predict any large/overall changes in the structure.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

There is an example of using Rotamers in the Structure Analysis and Comparison tutorial.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 25, 2019, at 2:00 PM, Joshua Plank <jplan002 at ucr.edu> wrote:
>
> Hi,
> I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible?
> thanks,
> Josh


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