VMD-L Mailing List

From: Luca UvA (lghiring_at_science.uva.nl)
Date: Thu Feb 06 2003 - 05:04:21 CST

Hi John,
            first of all thanks about the quick answer and the useful hint
about the rapresentation. Now I understand why "dynamic bonds" works so. I'd
like to have that plug-in for multi-frame xyz, since it seems the easiest
and most practical way for my problem. For me is much more easier to deal
with a c program operating on an ASCII trajectory file than with a tcl
script, furthermore I do not need to exploit the features of a pdb format. I
have vmd on a pc with linux-OpenGl machine. I also have it on win xp, but it
seems there there is no xyz.

Regards,
Luca

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Luca UvA" <lghiring_at_science.uva.nl>
Cc: <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, February 04, 2003 5:01 PM
Subject: Re: different colors

>
> 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
> 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
>