VMD-L Mailing List

From: Christian Seitz (cseitz_at_ucsd.edu)
Date: Wed Jun 29 2022 - 18:23:55 CDT

Hi Josh,

Thanks for showing how to cluster through VMD. One of my bosses first used
QR structure clustering, and because of that, my other boss wants me to
repeat it for a new system. This was the rationale for trying to figure it
out. This must be a simple question, but how do I access the multiseq.tcl
script that you reference? I am relatively familiar with VMD and have been
looking into the MultiSeq GUI, but have not used tcl scripts from plugins
before, and don't know where to look for them.

If I can't readily figure this out I will simply use the VMD measure
command as you showed above, or some other form of clustering that I am
already familiar with. Thanks!

Best,
Christian

On Tue, Jun 28, 2022 at 2:03 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> Hi Christian,
>
>
>
> Any reason you don’t want to use the clustering algorithm available from
> the measure command?
> https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html
> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html__;!!Mih3wA!HIm8lNGOEb-Z_IjJBV4jhBlJ_ygBDuQkNsDGNKht7Zs2N440N9ckGq-WJFgY2Iv06JxTn88Ajl4Mobkx$>
>
>
>
> If you have everything loaded up already, you can increase the number of
> desired clusters sequentially until every structure is classified.
>
>
>
> set psel [atomselect top “protein and backbone”]
>
> set numclusters 5
>
> set clustering [measure cluster $psel num $numclusters distfunc fitrmsd
> cutoff 2.0]
>
> while { [llength [lindex $clustering end]] > 0 } {
>
> #Add more clusters.
>
> set numclusters [expr {$numclusters + [llength [lindex $clustering end]] /
> [llength [lindex $clustering end-1]]}]
>
> #Cluster again
>
> set clustering [measure cluster $psel num $numclusters distfunc fitrmsd
> cutoff 2.0]
>
> }
>
>
>
> Otherwise, it looks like multiseq is using libbiokit under the hood to do
> its QH, clustering. In multiseq/multiseq.tcl (its in the plugins tree in a
> normal vmd installation), I think you are looking for the
> “getNonRedundantStructures” calls. libbiokit can *also* do QR
> factorization, but based on the code, I think it only does this for
> sequences.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Christian Seitz <
> cseitz_at_ucsd.edu>
> *Date: *Tuesday, June 28, 2022 at 4:12 PM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: MultiSeq QR structure factorization on the command line
>
>
>
> Hello,
>
>
>
> I am trying to use MultiSeq's structure QR factorization, to select
> structurally distinct protein conformations out of a trajectory. This can
> be done in the VMD GUI with a limited number of pdb files, but can it be
> done on the command line? I have very long trajectories (100,000 frames)
> and loading in all these frames to the MultiSeq GUI would take over a week
> at my current rate. Considering I have multiple systems, I'm looking for a
> faster way to do this. I see that years ago someone asked the same question
> (https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17207.html
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17207.html__;!!HXCxUKc!xm7NVJYM4RD_4MvxfZH-ixJ5VQYr3j2RAibmwvsunURp08Qkslv0s56ZPQDUdNa4XpHBJrOuLnu3CyM$>);
> 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>
>
>
>
>
> <https://urldefense.com/v3/__http:/www.linkedin.com/in/christianseitz21__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_O45H-x2Q$>
> 

-- 
*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!6xL6k-kIcSgwoLdf3G1hIhztzV51rRdq_mDAerINMWoDLMbw-tBY20yOIo61YK_guLb_IH0Tuw_cbrFrXw$ > and Amaro lab
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cseitz_at_ucsd.edu <cseitz_at_elon.edu>
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