VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 03 2014 - 01:01:49 CST

Sure, I'm not against the pdb format and use it within its limitations.
Please notice that the original meaning and use of the pdb format was
completely different from today. So the pdb format has a large amount of
disadvantages: It's limiting the number of atoms and more dramatically
residues, the coordinate range and as a ascii with large amount of
redundancy and empty columns, it is very large on your disk. So it would be
reasonable to store all the structures in a different smaller format, too,
if your problem is loading speed. As you didn't really told us where your
problem with the files is, we can't know if it is just your disc space
running out or loading the files into VMD is too slow for you, or whatever.
In any case you should compare the effort of changing VMDs source against
trying other formats, depending on what your problem actually is, buying
another HDD may already solve your problem.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Bennion, Brian [mailto:Bennion1_at_llnl.gov]
> Gesendet: Sonntag, 2. Februar 2014 00:28
> An: Norman Geist
> Betreff: RE: vmd-l: wrapper for VMD to read compressed .xz files
>
> Obviously, however I am not the creator of these files. but like it or
> not pdb seems to be the common structural currency of the day.
>
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Norman Geist [norman.geist_at_uni-greifswald.de]
> Sent: Saturday, February 01, 2014 1:06 PM
> To: 'Axel Kohlmeyer'
> Cc: VMD Mailing List
> Subject: AW: vmd-l: wrapper for VMD to read compressed .xz files
>
> 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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> = 

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