From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Thu Nov 17 2005 - 12:11:20 CST

Hi!

the rmsdtt2 plugin does all againts all comparisions:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/rmsdtt2.html

Best,

Luis

Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu

andrea spitaleri said the following on 11/17/05 03:50:
> Hi all,
> first this is my first script in tcl/vmd and I need of course feedback.
> I have 100 structures and I want to calculate the rmsd in a such way:
> structure_1 structure_2 rmsd
> 1 2 rmsd12
> 1 3 rmsd13
> 1 4 rmsd14
> .......
> 1 100 rmsd1100
> 2 3 rmsd23
> 2 4 rmsd24
> .....
> and so on.
> Below there is a script but it does not work properly. Could someone
> help me to understand what is wrong in it. Second, to run it, do I need
> to run in vmd console or can I run in a shell like vmd -script
> script,without gui ?
>
>
> proc calculate_rmsd {}{
> for { set i 1 } { $i < 100 } { incr i } {
> # pro is the root of the name of my structures
> mol load pdb pro_i.pdb
> set sel1 [atomselect "backbone"]
> for { set j i+1 } { $j < 100 } { incr j } {
> set sel2 [atomselect j "backbone"]
> set rmsd [measure rmsd $sel1 $sel2]
> puts RMSD of $i $j is $rmsd
> }
>
> Thanks
>
> Regards,
>
> andrea
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
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