VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 23 2019 - 23:31:12 CDT

Hi,
  Have you worked through VMD tutorials that demonstrate simple scripting
with loops over frames etc yet? You should be able to adapt what you
learn in those scripts to loop over either frames or molecules to
perform the RMSD calculations you're interested in.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 19, 2019 at 07:14:51AM +0000, Almira Ovagimyan wrote:
> I'm trying to calculate RMSD of all of 11 proteins with each other.
>
> --------------------------------------------------------------------------
>
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Almira Ovagimyan <almira_ovagimyan_at_hotmail.com>
> Sent: Thursday, July 18, 2019 3:36 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Tcl
>
> Hi,
> I'm trying to calculate rmsd of two proteins on VMD TkConsole. However I
> have a lot of proteins to calculate. Here is what I use to calculate only
> for two proteins.
> set sel0 [atomselect 0 "backbone"]
> set sel1 [atomselect 1 "backbone"]
> set M [measure fit $sel0 $sel1]
> set sel0 [atomselect 0 "all"]
> $sel0 move $M
> set sel5 [atomselect 0 "resid 31 34 35 37 38 41 71 72 75 76 79 82 94 110
> 117 203 206 207 210 221 225 229"]
> set sel6 [atomselect 1 "resid 31 34 35 37 38 41 71 72 75 76 79 82 94 110
> 117 203 206 207 210 221 225 229"]
> measure rmsd $sel5 $sel6
> Can I get help for calculating rmsd for more than 2 proteins with a tcl
> script (for loop might be included)?

>
> 5APOs_RESs_c0.pdb rmsd: 2.1690
> 5APOs_RESs_c1.pdb
>
> 5APOs_RESs_c0.pdb rmsd: 1.6223
> 5APOs_RESs_c2.pdb
>
> 5APOs_RESs_c0.pdb rmsd: 2.0275
> 5APOs_RESs_c3.pdb
>
> 5APOs_RESs_c0.pdb rmsd: 2.5265
> 5APOs_RESs_c4.pdb
>
> 5APOs_RESs_c2.pdb rmsd: 2.4175
> 5APOs_RESs_c1.pdb
>
> 5APOs_RESs_c1.pdb rmsd: 2.665
> 5APOs_RESs_c3.pdb
>
> 5APOs_RESs_c1.pdb rmsd: 2.3299
> 5APOs_RESs_c4.pdb
>
> 5APOs_RESs_c2.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> 5APOs_RESs_c2.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
> 5APOs_RESs_c3.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
>
>
> 3000ns.c0.pdb rmsd:
> 5APOs_RESs_c0.pdb
>
> 5APOs_RESs_c0.pdb rmsd:
> 3000ns.c1.pdb
>
> 5APOs_RESs_c0.pdb rmsd:
> 3000ns.c2.pdb
>
> 5APOs_RESs_c0.pdb rmsd:
> 3000ns.c3.pdb
>
> 5APOs_RESs_c0.pdb rmsd:
> 3000ns.c4.pdb
>
> 3000ns.c1.pdb rmsd:
> 5APOs_RESs_c1.pdb
>
> 3000ns.c2.pdb rmsd:
> 5APOs_RESs_c1.pdb
>
> 3000ns.c3.pdb rmsd:
> 5APOs_RESs_c1.pdb
>
> 3000ns.c4.pdb rmsd:
> 5APOs_RESs_c1.pdb
>
> 3000ns.c1.pdb rmsd:
> 5APOs_RESs_c2.pdb
>
> 3000ns.c2.pdb rmsd:
> 5APOs_RESs_c2.pdb
>
> 3000ns.c3.pdb rmsd:
> 5APOs_RESs_c2.pdb
>
> 3000ns.c4.pdb rmsd:
> 5APOs_RESs_c2.pdb
>
> 3000ns.c1.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> 3000ns.c2.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> 3000ns.c3.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> 3000ns.c4.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> 3000ns.c1.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
> 3000ns.c2.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
> 3000ns.c3.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
> 3000ns.c4.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
>
> 3000ns.c0.pdb rmsd:
> 3000ns.c1.pdb
>
> 3000ns.c0.pdb rmsd:
> 3000ns.c2.pdb
>
> 3000ns.c0.pdb rmsd:
> 3000ns.c4.pdb
>
>
> 3000ns.c1.pdb rmsd:
> 3000ns.c2.pdb
>
> 3000ns.c1.pdb rmsd:
> 3000ns.c3.pdb
>
> 3000ns.c1.pdb rmsd:
> 3000ns.c4.pdb
>
> 3000ns.c2.pdb rmsd:
> 3000ns.c3.pdb
>
> 3000ns.c2.pdb rmsd:
> 3000ns.c4.pdb
>
>
>
> 3000ns.c0.pdb rmsd:
> APO1-Last.pdb
>
> 3000ns.c1.pdb rmsd:
> APO1-Last.pdb
>
> 3000ns.c2.pdb rmsd:
> APO1-Last.pdb
>
> 3000ns.c3.pdb rmsd:
> APO1-Last.pdb
>
> 3000ns.c4.pdb rmsd:
> APO1-Last.pdb
>
> APO1-Last.pdb rmsd:
> 5APOs_RESs_c0.pdb
>
> APO1-Last.pdb rmsd:
> 5APOs_RESs_c1.pdb
>
> APO1-Last.pdb rmsd:
> 5APOs_RESs_c2.pdb
>
> APO1-Last.pdb rmsd:
> 5APOs_RESs_c3.pdb
>
> APO1-Last.pdb rmsd:
> 5APOs_RESs_c4.pdb
>
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> 5APOs_RESs.c0.pdb
> 5APOs_RESs.c1.pdb
> 5APOs_RESs.c2.pdb
> 5APOs_RESs.c3.pdb
> 5APOs_RESs.c4.pdb
> 3000ns.c0.pdb
> 3000ns.c1.pdb
> 3000ns.c2.pdb
> 3000ns.c3.pdb
> 3000ns.c4.pdb
> APO1-Last.pdb
>
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> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/