VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Sat Feb 01 2014 - 15:06:26 CST

Best option would be to not use pdb at all cause of its large amount of
redundancy and better find another optimized format that doesn't need
compression, maybe a binary one.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Samstag, 1. Februar 2014 00:49
> An: John Stone; Bennion, Brian; vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: wrapper for VMD to read compressed .xz files
>
> well, on a linux (or similar) machine, you could also write something
> more generic like the zlibc wrapper. https://zlibc.linux.lu/index.html
> this will transparently support reading compressed files via
> LD_PRELOAD and is completely application agnostic.
>
> axel.
>
> On Fri, Jan 31, 2014 at 5:43 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > If you wanted to, you could hack the PDB reader plugin to
> > do this for you, and replace the standard one with yours.
> > That would be pretty straightforward I think.
> >
> > Cheers,
> > John
> >
> > On Fri, Jan 31, 2014 at 10:33:18PM +0000, Bennion, Brian wrote:
> >> Hello,
> >>
> >> I have approximately 300K pdb files that are compressed with xz.
> I have a
> >> wrapper for my "less" that decompresses on the fly. Is there
> something
> >> similar that anyone else has done with vmd?
> >>
> >> Brian
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> International Centre for Theoretical Physics, Trieste. Italy. 

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