VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Thu Nov 17 2005 - 04:14:40 CST

Reading Luc's reply, I think I misinterpreted Andrea's e-amail.
I was thinking in terms of a trajectory, not on single snapshots.
N.
----- Original Message -----
From: <l.spitzer_at_fr.fournierpharma.com>
To: "andrea spitaleri" <spitaleri.andrea_at_hsr.it>
Cc: <vmd-l_at_ks.uiuc.edu>
Sent: Thursday, November 17, 2005 9:52 AM
Subject: vmd-l: Réf. : vmd-l: calculate rmsd in a loop:feedback [sorry if
you get it twice]

>
>
>
>
> Hi Andrea!
>
> I am not a specialist in vmd-tcl programming but I think there are a few
> problem in your script :
> first, this line : mol load pdb pro_i.pdb shouldn't you add a "$" before
> "i"?
> Then, when you do your first selection ($sel1), you don't precise the name
> of the molecule on which you do the selection (set sel1 [atomselect
> "backbone"]).
> Then, when you initialize your "sel2" variable, what do you use as a
> protein? I mean, you have : "set sel2 [atomselect j "backbone"]", it means
> you select atoms from "j" where j is a number, not a molecule! shouldn't
> you first load the molecule "pro_$j.pdb" as you do with your "sel1" ? Do
> you understand what I mean?
>
> To answer your question, I think you may use VMD without the GUI to launch
> your script, using command "vmd -dispdev text" in your shell, so you won't
> have the GUI.
>
> I hope this will help you,
>
> Regards,
>
> Luc SPITZER
>
>
>
>
>
> andrea spitaleri
> <spitaleri.andrea Pour : vmd-l_at_ks.uiuc.edu
> @hsr.it> cc :
> Envoyé par : Objet : vmd-l: calculate
rmsd in a loop:feedback [sorry if you get it twice]
> owner-vmd-l_at_ks.ui
> uc.edu
>
>
> 17/11/2005 09:50
>
>
>
>
>
>
> 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)
> Get Firefox!
> -------------------------------
>
>
>
>
>
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