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From: Almira Ovagimyan (almira_ovagimyan_at_hotmail.com)
Date: Fri Jul 19 2019 - 02:14:51 CDT

I'm trying to calculate RMSD of all of 11 proteins with each other.
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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)?