VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 24 2003 - 19:27:32 CDT

Ran,
  One possibility I've been kicking around is to optionally read in
atom radii from Charm parameter files etc, if we can come up with a script
or plugin to do so. I"m guessing we'd start with a script of some sort.
We recently had other needs in this regard in the process of developing
a plugin for running APBS electrostatics calculations from within VMD,
since they need a "pqr" file which is a hacked version of PDB with
charge and radii added in place of two of the normal columns.
You can set the radii with a simple Tcl script that modifies
the radii via an atom selection, but other than these "pqr" files, I don't
know of too many file formats that provide radii information. If you look
around, most other viz programs are using various heuristics to assign
atom radii since most files don't provide it. If you're interested in
assigning radii yourself using a script, let me know and I can give
you a few pointers on that.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 08, 2003 at 10:13:43AM +0200, Ran Friedman wrote:
> 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
>
> --
> ------------------------------------------------------
> 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