From: Alison Grinthal (
Date: Tue May 29 2007 - 15:58:18 CDT

I'm new to VMD and am wondering if someone can provide advice on the best way
to do the following:

I have a trajectory file from a pulling simulation, and I'm trying to compare
the structural details of the initial, early, and final stages. So first I'm
wondering how to overlay structures from different frames, while specifying
which segment to base the alignment on. I'd also like to compare the structure
of a given trajectory frame with the published structure of the same protein
crystallized in complex with another subunit (which isn't present in the
simulated structure's psf file; it's a different pdb file).

More specifically, the protein is composed of sequential repeats, and I'd like
to analyze how the orientation between adjacent repeats changes with pulling.
To do this, I'd like to look at 2-repeat units from different frames, but align
them based only on the first repeat, so I can see how the orientation of the
second repeat changes relative to the first.

Thanks very much for any advice.