From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Thu Feb 09 2006 - 12:20:44 CST

On Thu, 9 Feb 2006, Joseph Fernandez wrote:

JF> Hi:

joe,

JF>
JF> I have multiple files that I would like to load in
JF> VMD. These are compressed (gzip) AMBER trajectory
JF> files. Due to space limitation on my machine, I would
JF> like to systematically uncompress a file, load the
JF> file, and compress the file within a tcl script; e.g.

if you are running on one of the supported systems,
you may want to try zlibc ( http://zlibc.linux.lu/ )
which does this on the fly. just preload the library
and try to open the file without the .gz.

if not, see below.

JF> JF> gunzip md_eq_001_nowat.mdcrd.gz
JF> mol addfile md_eq_001_nowat.mdcrd type crdbox first 0
JF> last -1 stride 1
JF> gzip md_eq_001_nowat.mdcrd
JF> gunzip md_eq_001_nowat.mdcrd.gz
JF> mol addfile md_eq_001_nowat.mdcrd type crdbox first 0
JF> last -1 stride 1
JF> gzip md_eq_001_nowat.mdcrd
JF> ...etc
JF>
JF> However, I get the following message in the Tk windown
JF> when I run the script:
JF>
JF> invalid command name "gunzip"
JF>
JF> How could I invoke the gunzip command within a tcl
JF> script.
JF>
JF> I look forward to you assistance on this matter.

this is a TCL 'feature'. generally you are spawning
subprocesses with 'exec', so doing:

exec gunzip md_eq_001_nowat.mdcrd.gz

should give you the desired result.
the on-the-fly decompression is preferable,
as it also is _much_ faster on networked
filesystems etc.

regards,
    axel.

JF>
JF> Joe
JF>
JF>
JF>
JF>
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JF>

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.