VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 04 2003 - 10:01:19 CST

Hi Luca,

On Tue, Feb 04, 2003 at 11:50:40AM +0100, Luca UvA wrote:
> Hi,
> I have the following problem. I'd like to visualize a trajectory of a liquid sample, in which, in every frame, atoms should have different colors related to certain properties. For example, as simplest thing, even having a sample of P atoms, I'd like to have, e.g., red the 4-fold coordinated, green the 3-fold, and so on. Normally I can generate a multi frame pdb file, I tried to simply change the name of the atom in different frame, but the kind of atom it is given on the first frame then it is preserved.

Yes, this is correct, VMD holds on to the atom names etc from the first
structure in a PDB. In order to change the coloring over a time, you'll
probably need to use a script, since your coloring will be unrelated to
atom coordinates etc.

> I tried generating an xyz file, but I cannot find the way to load multiframes.

We have a new 'xyz' plugin that should handle multi-frame files.
Let me know what type of machine you're using and I can provide
you with a new xyz plugin that'll most likely cure that issue for you.

> Is there a file format supported that allow this or a script that can do that after a, say, pdb is loaded on VMD?

A Tcl script would be your best bet. You can have the Tcl script
trace the active frame, and update the coloring scheme(s) used as
VMD animates. Here are a few documentation links of interest for what
you'd like to do.

Tcl callbacks, vmd variables you can "trace" on:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node143.html#7065

Overriding a color category:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node188.html

See the 'betacolor distance' example script near the bottom:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node180.html

> Furthemore, it is essential that I can load in parallel the same trajectory twice since I need both the dynamic bonds feature and the VDW, to have balls marking non bonded atoms: this is possible with a pdf file, but it seems not for xyz (I use both Win and Linux version).

There shouldn't be any need to load the trajectory twice, instead, just
create two representations, one VDW and one dynamic bonds. This is exactly
why I implemented the dynamic bonds the way I did, this way you can get a
CPK or Licorice-like representation very easily.

Let us know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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