VMD-L Mailing List

From: #WONG CHEE HOW# (P7443050C_at_ntu.edu.sg)
Date: Thu Sep 19 2002 - 02:36:27 CDT

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