VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 21 2018 - 13:07:40 CST

On Wed, Feb 21, 2018 at 1:18 PM, Dive, Aniruddha Mukund <
aniruddha.dive_at_wsu.edu> wrote:

> Thanks John for your suggestion,
>
>
> I understand the use of $env(VARIABLE) prior to launching VMD.
>

No, you do not. $env(VARIABLE) is the syntax for accessing a
previously-set environment variable in Tcl, i.e. *after* launching VMD.

> To avoid the use of that I am writing the value of variable to a "tmp"
> file and then I read the value of variable from the "tmp" file in the TCL
> script. I am able to successfully read the value of the variable from the
> tmp file in the TCL script. The error I face is that VMD is not able to
> load the trajectory file through the below command in the TCL Script
>
>
> mol load pdb Si_S_config$data.pdb
>
>
> Below is the error I get with the attached TCL Script:
>
> file16
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
>
> Si_S_config2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> .pdb
> ERROR) Could not read file Si_S_config2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> ERROR) 2
> Unable to load structure file Si_S_config2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> 2
> .pdb
> There is no 'top' molecule in atomselect's 'molId'
>
> The file name I want to load is Si_S_config2.pdb, but somehow the file
> name ends after$data and it doesnot read the filename as Si_S_config2.pdb
> but instead as Si_S_config2 and .pdb separately. Kindly let me know how to
> get around this issue? Is this issue due to non declaration of
> $env(VARIABLE)?
>
>
> Regards,
>
> *Aniruddha M Dive*
>
> PhD student
>
> School of Mechanical and Materials Engg.
>
> Washington State University
> ------------------------------
> *From:* John Stone <johns_at_ks.uiuc.edu>
> *Sent:* Tuesday, February 20, 2018 8:49:00 AM
> *To:* Dive, Aniruddha Mukund
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: VMD TCL Script to save last frame of a trajectory
> using bash+tcl scripts
>
> Hi,
> You need to use Tcl's $env(VARIABLE) interface to obtain environment
> variables set in external command shells prior to launching VMD.
> Similarly, when using bash/bourne shells, you will need to use
> "export FOO=BAR" to ensure that the variable propagates to subshells
> and child processes like the VMD instance(s) you want to run.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 19, 2018 at 10:37:33PM +0000, Dive, Aniruddha Mukund wrote:
> > Hi All,
> >
> > I am trying to make a bash script which will traverse through various
> > directories and save the coordinates of the last frame from a
> trajectory
> > in each of the directory. I have made a bash script attached hereby to
> > help me traverse through different directories and along with that I
> have
> > made another tcl script to save the coordinates of the last frame
> from the
> > trajectory. The TCL script works fine without the variable introduced
> > while loading the molecule. But when I introduce a variable in the
> name of
> > the molecule in the TCL script, the script is not able to recognize
> the
> > molecule and hence cannot load the molecule.
> >
> > Kindly let me know what could be a possible reason for this?
> >
> > Aniruddha M Dive
> >
> > PhD student
> >
> > School of Mechanical and Materials Engg.
> >
> > Washington State University
>
> > set f [open tmp]
> > set data [read $f]
> > close $f
> > puts "Si_S_config$data.pdb"
> > mol load pdb Si_S_config$data.pdb
> > [atomselect top all frame last] writepdb Si_S_config_$data.pdb
> >
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin