VMD-L Mailing List

From: Ran Friedman (ran_at_hemi.tau.ac.il)
Date: Wed Oct 08 2003 - 03:13:43 CDT

Hi,

Thanks a lot for the information. I currently use mainly the standard pdb
format (not including COLO) and GROMACS. However, if there's another format
that VMD reads and that will enable me to modify the VDW radius information,
I'll be happy to use it.

Ran.

John Stone wrote:

> Dear Ran,
> Regarding the nonstandard Rasmol COLO records, no, at this time
> VMD doesn't know how to read those, and they would just be ignored by
> the PDB plugin. Also, while it is possible to teach the PDB plugin
> to read those and store them, we don't presently have an interface
> in the VMD plugin API nor in VMD itself to use such information for
> anything, so we'd have to add code in several places to make the COLO
> records useful to VMD, even after we would teach the PDB plugin to
> read them.
>
> I'll have to get back to you on which specific plugins read in
> VDW radii as I don't know off the top of my head.
>
> At best, its a relatively subset of the available file
> formats since many file format sdo not provide that information, so
> in many cases VMD does have to guess. You can of course override
> the default radii with a simple Tcl script if you wish.
>
> What file format(s) are you working with by the way?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 07, 2003 at 05:47:50PM +0200, Ran Friedman wrote:
> > Hello all,
> >
> > I've previously asked how to find the VDW radii that VMD assigns to
> > atoms. John replied that in absence of this information from the
> > structure files that are loaded, VMD "guesses" based on the string atom
> > names.
> >
> > What I'd like to know now is what input formats enable VMD to find this
> > information. Furthermore, can VMD read the COLO record type of a PDB
> > file like rasmol?
> >
> > Ran.
> >
> > --
> > ------------------------------------------------------
> > Ran Friedman
> > Laser laboratory for fast reactions in biology
> > Department of biochemistry
> > Faculty of life sciences
> > Tel-Aviv university
> > 972-3-6409824
> > ------------------------------------------------------
> >
> >
>
> --
> 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 

--
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Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
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