From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Thu Nov 17 2005 - 04:14:01 CST

Hi all,
thanks for your quick replies. Yes Luc, you are right! I forgot some $.
I changed in :
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 $i "backbone"]
    for { set j i+1 } { $j < 100 } { incr j } {
        mol load pdb pro_$j.pdb
        set sel2 [atomselect $j "backbone"]
        set rmsd [measure rmsd $sel1 $sel2]
        puts RMSD of $i $j is $rmsd
    }
    }
}

and it loops but it doesn't print the rms, just info>. At the end it says:
invalid command name "}"
not clear where...at least to me :)
I am not quite convinced on the lines set sel1 [atomselect $j "backbone"]

Regards,
andrea

l.spitzer_at_fr.fournierpharma.com wrote:

>
>
>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!
>-------------------------------
>
>
>
>
>

-- 
-------------------------------
Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
-------------------------------