VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Wed Jun 29 2022 - 20:47:32 CDT

Hi Christian,

The multiseq.tcl file is just in the plugins directory with everything
else, and is what defines the gui you have been using so far. In my
install on a linux workstation they'd be installed under
/usr/lib/vmd/plugins, with multiseq (and many others) living in the
noarch subdirectory. This varies depending on how you installed VMD. The
user guide has more information on how to determine the installation
directory and what the defaults are on windows platforms.
https://www.ks.uiuc.edu/Research/vmd/current/ug/node245.html

-Josh

On 6/29/22 19:23, Christian Seitz wrote:
> 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 <mailto:cseitz_at_elon.edu>
>
>
>
> <https://urldefense.com/v3/__http:/www.linkedin.com/in/christianseitz21__;!!DZ3fjg!-ZJB_XmNsDaOPPw1Sr90_AG-N_MKojEblBY58RChyd6avXFmS-qxJRoHQ9U-2whd8N6Ttdp88_O45H-x2Q$>
>
>
>
> --
> *Christian Seitz*
> PhD Candidate, Biochemistry & Biophysics | UC-San Diego
> NSF GRFP Fellow, Amgen Scholar
> McCammon lab
> <https://urldefense.com/v3/__https://mccammon.ucsd.edu/__;!!HXCxUKc!07BjLbaa4_k7tsvULXHN1m43xcprODUtz6Ab1NwRNi58NBQon3bPJkt2wXcem_FHAACUFwM4tvCgMlU$> and Amaro
> lab
> <https://urldefense.com/v3/__https://amarolab.ucsd.edu/__;!!HXCxUKc!07BjLbaa4_k7tsvULXHN1m43xcprODUtz6Ab1NwRNi58NBQon3bPJkt2wXcem_FHAACUFwM4o3wttFg$>
> cseitz_at_ucsd.edu <mailto:cseitz_at_elon.edu>
> https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!DZ3fjg!-jt600_SZoPdd4ut_GUwhNsryrI6wd7bWi77jrWpKrKKEsIYAQM60E_W6v6Y2wB8WkPqqmF5F2WHsZhg5Ac$
>
> <https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!HXCxUKc!07BjLbaa4_k7tsvULXHN1m43xcprODUtz6Ab1NwRNi58NBQon3bPJkt2wXcem_FHAACUFwM4zItcjOo$>