VMD-L Mailing List

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Aug 19 2005 - 16:26:32 CDT

I'm trying to overlay two drug molecules in a binding site of a DNA
strand from a pdb file. I've read in the manual that you can overlay
structures in VMD, but I've never been able to understand how to get it
to work. I've been getting help with this from a friend who knows
MIDAS. In MIDAS it's relatively easy, you give it the match command
and then pick the four atoms of each structure you want to match.
However, the computer that has MIDAS is not convenient to access ( a
VERY old SGI) and I'd like to be able to do something similar on my
Mac. Has anyone done this before and would someone be willing to talk
me through it?

Thank you in advance,

Kara Di Giorgio
University of the Pacific