[Chimera-users] [EXTERNAL] Re: RMSF calculations

Reza Khayat rkhayat at ccny.cuny.edu
Thu May 12 14:15:29 PDT 2022

Hi Elaine and Eric,

I was unaware that ChimeraX did this. I now have a script for ChimeraX; however, I have the problem of wanting to calculate the RMSF for non-standard residues (glycans). The sequence chain command does not extract the glycan sequence. Is it possible to calculate the RMSF of glycans with ChimeraX? Thanks.

Best wishes,

Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Thursday, May 12, 2022 12:50 PM
To: Reza Khayat
Cc: chimera-users at cgl.ucsf.edu
Subject: [EXTERNAL] Re: [Chimera-users] RMSF calculations

Hi Reza,
As Elaine said, this may be simpler in ChimeraX.  Nonetheless, if you have a fasta file (or equivalent) with your sequence in it, all members of the ensemble should automatically associate with the sequence when you open it.  Nonetheless, the remaining steps (showing RMSD header, saving attributes file) do not have command equivalents and would require resorting to some moderately difficult Python code.  I don't know if you'd prefer to do that or switch this to ChimeraX where it's more directly supported.  I can provide guidance on the former if you really want to stick with Chimera for some reason.


Eric Pettersen
UCSF Computer Graphics Lab

On May 12, 2022, at 7:40 AM, Reza Khayat via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:


I'm trying to write a script to perform the procedure described here:


Can someone help with the command line syntax for associating a structure with a defined sequence? Thanks.

Best wishes,

Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
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