VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 05 2004 - 01:18:01 CDT

Edward,
  The XYZ reader plugin doesn't do anything with the columns beyond the
XYZ coordinates presently. I hope to implement improvements to load these
values into new data fields eventually, but that isn't implemented yet.
In the mean time, it'd probably be easiest to parse these columns in a
Tcl script, loading them into the "User" data storage in VMD. It shouldn't
be very difficult to do, just a few lines of scripting to read the XYZ
file and parse out that last column of interest.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 04, 2004 at 04:25:50PM -0400, Edward J. Smiley Jr. wrote:
> Hello all,
> I am having some trouble trying to figure out how to color with this
> new user field. I have an xyz file (well, xmol actually) that is made
> up of numerous frames with the following format.
>
> >530590
> >Time = 0
> >C9 166.23 164.11 6.53 1.00
> >C9 167.14 163.06 6.96 1.00
> >etc. to line 530592
> >530590
> >Time = 1
> >C9 166.23 164.11 6.53 1.00
> >C9 167.14 163.06 6.96 0.00
> >etc.
>
> The last column represents the direction of the atom. If it is a 1
> then it is moving down, if it is a 0 then it is not moving or moving
> up. I have tried to figure out where this last column is put when VMD
> "converts" it from an XYZ. The user field only lists 0.00 and no other
> field list 1and 0. How does VMD handle a xyz file, does it convert it
> to a PDB somehow or just read it straight?
>
> You guys have a great program here!
> Thanks for any help,
> Ed Smiley 

-- 
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