VMD-L Mailing List
From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Thu Nov 17 2005 - 03:31:13 CST
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Hi Andrea, again ;-)
About the issue of running vmd in non gui mode.
You could use the comand vmd -dispdev text -e script -args arg1 arg2
This will run the comands under vmd issued in file scripts, and we could also parse some arguments to vmd also. These ones will be stored in the list variable argv.
Check it in vmd manual (1.8.3) pgs 165-167.
About the proc, I think that you need to work with the frame comand inside the atomselections, for this to work,
like set sel [atomselect top backbone frame $nframe].
Best regards,
Nuno
----- Original Message -----
From: andrea spitaleri
To: vmd-l_at_ks.uiuc.edu
Sent: Thursday, November 17, 2005 8:50 AM
Subject: vmd-l: calculate rmsd in a loop:feedback [sorry if you get it twice]
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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- Next message: l.spitzer_at_fr.fournierpharma.com: "Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Previous message: andrea spitaleri: "calculate rmsd in a loop:feedback [sorry if you get it twice]"
- In reply to: andrea spitaleri: "calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Next in thread: Axel Kohlmeyer: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
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