[Chimera-users] RMSF calculations

[Elaine Meng]

Hi Reza,
There is no Chimera command to do the association, sorry.  That there are GUI  or menu actions without commands are a limitation of Chimera that we are actively addressing in ChimeraX.

There must be some python code that would do it, but somebody else would have to advise on that.

In ChimeraX instead of Chimera, you can do all the steps of (B) in that procedure with commands, namely: open, matchmaker, sequence chain, sequence associate, sequence header, save <filename> attrName seq_rmsd  ... see help pages:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html><https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

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


> On May 12, 2022, at 7:40 AM, Reza Khayat via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I'm trying to write a script to perform the procedure described here:
> 
> https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-March/013247.html
> 
> Can someone help with the command line syntax for associating a structure with a defined sequence? Thanks.
> Best wishes,
> Reza 
>