VMD-L Mailing List

From: Fred Moore (moore_at_whitman.edu)
Date: Tue Mar 27 2007 - 14:06:21 CDT

2nd posting from a newbie to VMD.

I'm running the latest version on a macintosh pb 12" powerpc with the
latest osx.

I'm trying to view and animate a .pdb file full of chloroform
molecules. 475 molecules per frame, 2500 frames. The .pdb file names
the atoms in each molecule:

C1, CL1, CL2, CL3, H

Those names show up properly when I go to Graphics->Representations
and look under "keyword".

In trying to view and represent these critters I've used different
representations.

A: style: CPK, color:Element, Selection: all
B: A: style: CPK, color:Element, Selection: { same residue as (name
C1 and z>19 and z<61)}
C: A: style: licorice, color:Name, Selection: { same residue as (name
C1 and z>19 and z<61)}

I have turned off the display of representation "A" by double
clicking on it. B and C are turned on.

Here's the newbie question: Should those two representations be
showing the same molecules? I must be missing something because
they're not.

It's not the coloring or drawing method either, as I can make them
identical and the two representations still show different molecules.

What am I missing?

Thanks in advance,

Fred M.