VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 11 2002 - 10:26:13 CDT

Dear Stephane,
  At one point (a long time ago) the Charmm/NAMD DCD trajectory reader
code in VMD was capable of reading from pipes and could invoke 'zcat' to
uncompress files on the fly. This was an undocumented feature at the time
and it got dropped when we ported to Microsoft Windows. It should not be
terribly hard to modify the trajectory reader plugins to do this again,
since the new code is quite a bit cleaner than the old code was. If
you're interested in giving it a try, you will need to modify the
code for the trajectory plugin(s) of interest, and then you should be
able to load your modifified plugin in place of the standard one for
testing. You'll want to use popen() to accomplish reading the output
from zcat/gzcat, etc.

Longer term, we have been working (slowly) on creating a new compressed
trajectory file format here. Using a combination of several compression
techniques we can already achieve much higher compression ratios than is
possible with plain compress/gzip. It'll be a while before we're ready
to make this available (lots of work to do still), but this will ultimately
be the best way to go, and is the reason why we haven't spent much time
on implementing built-in compress/gzip solutions in VMD.

  John

On Thu, Jul 11, 2002 at 10:17:41AM +0200, Stéphane Teletchéa wrote:
> I am using VMD to see amber trajectories, as it is a multi-platform software,
> and of course the cutting-edge one.
> Would it be difficult to read compressed files (gzip ou Z-compressed), as it
> saves some work space on my HD ?
> For the moment, i decompress it manually, but as zcat does the trick, how can
> it be/i include it in vmd.
> i'm using vmd-1.8a16.
> Stef 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078