VMD-L Mailing List

From: l.spitzer_at_fr.fournierpharma.com
Date: Thu Nov 17 2005 - 03:52:05 CST

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)
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