VMD-L Mailing List

From: Christian Seitz (cseitz_at_ucsd.edu)
Date: Tue Jun 28 2022 - 14:07:41 CDT

Hello,

I am trying to use MultiSeq's structure QR factorization, to select
structurally distinct protein conformations out of a trajectory. This can
be done in the VMD GUI with a limited number of pdb files, but can it be
done on the command line? I have very long trajectories (100,000 frames)
and loading in all these frames to the MultiSeq GUI would take over a week
at my current rate. Considering I have multiple systems, I'm looking for a
faster way to do this. I see that years ago someone asked the same question
(https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17207.html); the
multiseq.tcl referenced in that answer is not included in the tutorial, and
the tcl script that is included does not use factorization. Has there been
any progress on making MultiSeq scriptable? Or is there a better way to
accomplish this? Thanks for your help!

Best,
Christian 

-- 
*Christian Seitz*
PhD Candidate, Biochemistry & Biophysics | UC-San Diego
NSF GRFP Fellow, Amgen Scholar
McCammon lab <https://urldefense.com/v3/__https://mccammon.ucsd.edu/__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_Pv_VLnMw$ > and Amaro lab
<https://urldefense.com/v3/__https://amarolab.ucsd.edu/__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_OeZYC5NA$ >
cseitz_at_ucsd.edu <cseitz_at_elon.edu>
[image: https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_O45H-x2Q$ ]
<https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_O45H-x2Q$ >