VMD-L Mailing List

From: l.spitzer_at_fr.fournierpharma.com
Date: Thu Nov 17 2005 - 04:50:45 CST

Re-Hi! :-p

You should add quotes after your "puts" command (like puts "RMSD of $i $j
is $rmsd" ).
Then I just saw a little problem you may have : the first molecule loaded
in VMD has number 0, and you begin your sel1 with [atomselect $i
"backbone"] where i=1...so the first RMSD cannot be calculated, as you do
your selection with an un-existing protein...(it begins with [atomselect 1
"backbone"] and the molecule 1 doesn't exist...the first loaded molecule is
molecule 0!) do you see what I mean?
So you should begin your loop with set i 0...if you have a pro_0.pdb that
exists!!
At last, for your "set j i+1" you should better do something like "set j
[expr $i+1]" as it is a arithmetic expression.

Hope it will help you,

Regards,
Luc

                                                                                                                                       
                      andrea spitaleri
                      <spitaleri.andrea Pour : vmd-l_at_ks.uiuc.edu
                      @hsr.it> cc :
                      Envoyé par : Objet : vmd-l: Re: Réf. : vmd-l: calculate rmsd in a loop:feedback [sorry if you get
                      owner-vmd-l_at_ks.ui it twice]
                      uc.edu
                                                                                                                                       
                                                                                                                                       
                      17/11/2005 11:14
                                                                                                                                       
                                                                                                                                       

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!
-------------------------------