VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 07 2003 - 15:42:28 CDT

Ran,
  I forgot to mention, here's the official PDB file format spec,
in case you're curious what information they normally contain:
  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

Note that the Rasmol COLO record is non-standard, so other programs
that want to support it will have to read whatever docs the Rasmol/Chime
guys have put together on that.

This is the reason VMD has to guess VDW radii when loading only a PDB file,
no radii info is included in the ATOM record type:
  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html

Thanks,
  John Stone

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
> ------------------------------------------------------
>
> 

-- 
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