VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Aug 30 2005 - 13:43:29 CDT

On Tue, 30 Aug 2005, John Stone wrote:

hi,

i think this should already be in the mailing list archives:
on a selected number of operating system (e.g. linux) you can
actually make almost any program compatible with gzip (de)compression
by using zlibc and a smart use of the dynamic linker.

see: http://zlibc.linux.lu/ for more details.

best regards,
        axel.

JS> Hi,
JS> VMD doesn't recognize any compressed (gzip, zip, bz2, etc) file formats
JS> presently, though this is something I plan to support in a future version.
JS>
JS> John Stone
JS> vmd_at_ks.uiuc.edu
JS>
JS> On Tue, Aug 30, 2005 at 01:53:28PM +0200, Matthias Negri wrote:
JS> > Hi,
JS> > thanks a lot for the hint with crdbox.
JS> > I solved my problems now, with a great movie!!! .. it was really a small
JS> > problem! with an easy solution!!
JS> > But why is the crd plugin not recognising even gunzipped crd-files.. is
JS> > there an upgrade to expect or have I each time to unzip my crd-files??
JS> >
JS> > Thanksfulle, Matthias Negri
JS> > >
JS> > > Hi,
JS> > > If your trajectory was produced from a simulation with periodic boundary
JS> > > conditions, you will need to load it as a "crdbox". Try that end let us
JS> > > know if you still have trouble.
JS> > >
JS> > > John Stone
JS> > > vmd_at_ks.uiuc.edu
JS> > >
JS> > > On Mon, Aug 29, 2005 at 11:19:19AM +0200, Matthias Negri wrote:
JS> > > >
JS> > > > Hello, I have some problems while visualizing AMBER trajectories and
JS> > > > making movies from AMBER crd-files!
JS> > > > I'm working on a protein/DNA complex.
JS> > > > If I convert the crd-file in a pdb, the complex looks good, with
JS> > > > acceptable geometrical values, according to ptraj and Procheck. But if I
JS> > > > watch the crd file in VMD, the complex results distorted, specially one
JS> > > > DNA helix is changed in size,form AND position!! (and that even if it
JS> > > > doesn't result in the pdb. What's the reason for?
JS> > > > I nedd to create a good trajectory movie, but it seems harder as I
JS> > > > thought! Is it because of the DNA?
JS> > > >
JS> > > > Any help or hint would be appreceated, thanks in advance
JS> > > >
JS> > > > Matthias Negri
JS> > > > thias_at_scfarm.unibo.it
JS> > >
JS> > > --
JS> > > NIH Resource for Macromolecular Modeling and Bioinformatics
JS> > > Beckman Institute for Advanced Science and Technology
JS> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
JS> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
JS> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
JS> > >
JS> > >
JS> >
JS>
JS> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.