VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 07 2003 - 15:35:08 CDT

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
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