VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Tue Sep 25 2012 - 13:13:00 CDT

Hi Axel and Brian,

Many thanks for your help.

The script works fine now.

Best regards,

Flavio

--- On Tue, 9/25/12, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Subject: Re: vmd-l: Big DCD file help
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>, "VMD List" <vmd-l_at_ks.uiuc.edu>, "BrianBennion" <Bennion1_at_llnl.gov>
> Date: Tuesday, September 25, 2012, 6:54 PM
> 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
> >
> >
> >
>
>