[Chimera-users] RMSF calculations

Eric Pettersen pett at cgl.ucsf.edu
Thu May 12 09:50:05 PDT 2022

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> 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 <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 
> Reza Khayat, PhD
> Associate Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220512/ce5d6b4e/attachment.html>

More information about the Chimera-users mailing list