VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 25 2012 - 12:54:09 CDT

you have to write to the file in the proc myrmsd.

There is a great Tcl tutorial on www.tcl.tk. Highly recommended for all people doing scripting in vmd. It covers and explains all the stuff that the vmd users guide just glosses over and then some.

Axel. 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: flavio seixas <oivalf_nix_at_yahoo.com>
Sender: owner-vmd-l_at_ks.uiuc.edu
Date: Tue, 25 Sep 2012 09:56:05 
To: VMD List<vmd-l_at_ks.uiuc.edu>; BrianBennion<Bennion1_at_llnl.gov>
Subject: RE: vmd-l: Big DCD file help
Hi Brian, many thanks for your help.
I modify the scipt to:
proc myrmsd { frame } {
   global ref sel all
   $all move [measure fit $sel $ref]
   puts "$frame: [measure rmsd $sel $ref]"
 }
set mol [mol addfile CALDHmT178_wb_min4.coor type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
set outfile [open rmsd.dat w];
puts $outfile "[measure rmsd $sel $ref]"
bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd
bigdcd_wait
close $outfile
But it still does not work. 
Maybe is because I am not sure about how to "Make it global"
Sorry about the basic question, but I am not familiar with tcl scripts. I google it, but no clues about what to do...
Any advice?
Regards,
Flavio
--- On Tue, 9/25/12, Bennion, Brian <Bennion1_at_llnl.gov> wrote:
> From: Bennion, Brian <Bennion1_at_llnl.gov>
> Subject: RE: vmd-l: Big DCD file help
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>, "VMD List" <vmd-l_at_ks.uiuc.edu>
> Date: Tuesday, September 25, 2012, 5:43 PM
> 
> Not tested
> 
> Open a file
> Set fh1 [open "rmsd.plt" w]
> Make it global and in the proc add
> 
> puts $fh1 "$frame: [measure rmsd $sel $ref]"
> 
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]
> On Behalf Of flavio seixas
> Sent: Tuesday, September 25, 2012 8:16 AM
> To: VMD List
> Subject: vmd-l: Big DCD file help
> 
> Hi,
> 
> I am trying to calculate rmsd from my dcd files. The namd
> rmsd tcl script is working fine. Unfortunately the values
> appears listed in tk window and can not be copied at all.
> Is possible to put the rmsd values in a file?
> 
> This is my script:
> 
> 
> proc myrmsd { frame } {
>    global ref sel all
>    $all move [measure fit $sel $ref]
>    puts "$frame: [measure rmsd $sel $ref]"
>  }
> set mol [mol addfile CALDHmT178_wb_min4.pdb type pdb waitfor
> all] set all [atomselect $mol all] set ref [atomselect $mol
> "name CA" frame 0] set sel [atomselect $mol "name CA"]
> bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd bigdcd_wait
> 
> 
>