VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Sep 18 2006 - 14:19:28 CDT

On 9/18/06, tnels_at_sfu.ca <tnels_at_sfu.ca> wrote:
> thanks for your suggestions.
>
> I tried the one using 'env' and got an error:
>
> env VMDARGS='residue 5' vmd -dispdev text -e vmd_calls.txt -args
> $env(VMDARGS) backbone 0 1000 output.out
> -bash: syntax error near unexpected token `('
>
> do you know a different syntax for it?

sorry for the shorthand notation. you have to use
$env(VMDARGS) _within_ your alternative .vmdrc script
or the script that you are executing to get access to the string.
with the current csh based vmd script there is no way to
make -args work for arguments containing blanks without
changing the syntax.

axel.

>
> Nels
>
>
>
>
> On Sat, 16 Sep 2006 00:34:41 -0400 (EDT) akohlmey_at_cmm.chem.upenn.edu wrote:
> > On Fri, 15 Sep 2006 tnels_at_sfu.ca wrote:
> >
> > TN> Hi,
> > TN>
> > TN> I need to call VMD in text mode using the UNIX command line as
> follows:
> > TN>
> > TN> $ vmd -dispdev text -e vmd_calls.txt -args "residue 5" backbone 0
> > 1000 out_file
> > TN>
> > TN> the problem is that VMD won't accept the double quotes in this
> > call. My question is, can I
> > TN> pass a string containing spaces into -args as a single argument
> > somehow? I have tried
> > TN> several things like braces and backslash with no success.
> >
> > hi,
> >
> > the problem is in the csh code of the vmd script
> > and in part even in a deficiency of csh.
> >
> > the argv subscript error you can fix by loading the
> > vmd script into a text editor. look for
> >
> > foreach i ( $* )
> >
> > around line 140, and replace it with
> >
> > while ( $parmcount < $#argv )
> >
> > however this does not fix the problem of
> > the final $* splitting the argv array
> > at every blank. this can be only fixed with
> > rewriting the vmd script in bourne shell
> > and using "$@" instead of $* .
> >
> > however you can still pass the string you want selectively
> > be using the generic environment pasing.
> >
> > e.g. by starting VMD with
> >
> > env VMDARGS='text with blanks' vmd -dispdev text -args what ever
> >
> > and then refer to the variable with blanks via:
> >
> > $env(VMDARGS)
> >
> > cheers,
> > axel.
> >
> >
> >
> > TN>
> > TN> thank you
> > TN>
> > TN>
> >
> > --
> >
> =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> >
> =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
> >
>
>
> ------------------------------------------------------------
> Nels Thorsteinson
> Graduate Student
> CIHR Bioinformatics Training Program for Health Research
> (604)219-1754
> ------------------------------------------------------------ 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.