[chimerax-users] chimerax amino acid sequence

[Peter Steinhagen]

Hi Elaine,

thanks for your reply. I will try your suggestions.

Best,
Peter

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From: Elaine Meng<mailto:meng at cgl.ucsf.edu>
Sent: Sunday, August 9, 2020 12:13 PM
To: Peter Steinhagen<mailto:BA42_md21 at outlook.de>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] chimerax amino acid sequence
Importance: High

Hi Peter,
You can change an amino acid in a protein structure from one type to another with the "swapaa" command.  However, it's simply a sidechain replacement to let you do a first-order assessment of the possible effect (e.g. on local H-bonds or steric conflicts) and will not move or change any other atoms of the structure.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html>

You can also do a full-scale comparative modeling of a target protein via the Modeller web service (called from within ChimeraX) using the known protein structure as the template.  This requires registering at the Modeller web site to get a license key, which is free for academics.  You would also need a sequence alignment opened in ChimeraX (e.g. from Blast Protein or from a file you made in some other program) of the template and target sequence. See "Modeller Comparative" tool or command:

<http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
<http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/modeller.html#comparative>

This can also be used to model multiprotein complexes, as in this example on our "feature highlights" page:
<http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller>

Of course, there are dozens of programs and web services other than ChimeraX for protein structure and/or mutation effect prediction, so it may be worth investigating the alternatives depending on the needs of your project.  I don't have comprehensive knowledge on these so I couldn't give a specific recommendation.

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

> On Aug 8, 2020, at 2:11 PM, Peter Steinhagen <BA42_md21 at outlook.de> wrote:
>
> Hello,
> I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem?
> Thanks,
> Peter

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