VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 26 2002 - 16:38:08 CDT

Hi,
  The short version of how to do this is:
1) Use a tcl script to load your 200 PDB files, don't do it by hand.
2) Once you've loaded the PDB files, use the 'edit animation' form to save
   this trajectory out to a DCD file or other favorite trajectory format.
3) You can color atoms by making selections on them, or by coloring
   by their properties. If you have a strain value calculated for
   each atom, then you can color by this value by writing a Tcl script to load
   the strain values into the "beta" field for each atom. There's info on
   how to do this in the user's guide, look for the "betacolor_distance"
   script therein, and read the analysis and user defined graphics sections..

If you still need help after you've read through those sections of the
menual and so on, send us an email and we'll help you get this working.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 19, 2002 at 03:36:27PM +0800, #WONG CHEE HOW# wrote:
> Hi,
>
> I would like to find out if there is a way to use VMD to show different colours (or contour plot) for different atoms in a molecule. For instance, I have 100 atoms, and each of them having different strain energies. Can I then, say, use the lightest grey to represent the least strain energy and the darkest gray to represent the highest strain energy?
>
> Secondly, I am wondering if there is a simpler way to carry out animation in VMD. I normally have about 200 PDB files, each depicting a time-step. I then have to read all the 200 PDB files each at a time using the Edit Animation form, which is time consuming. As such, is there a simpler method for me? I only have the XYZ coordinates and PDB (using Babel to convert from XYZ) files. Finally, is there a way to say the animation in VMD instead of a movie? If not, I have to read in the 200 PDB files everytime I want to see the animation again.
>
> Cheers.
>
> C H WONG 

-- 
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