VMD-L Mailing List

From: Alison Grinthal (agrinth_at_fas.harvard.edu)
Date: Mon May 28 2007 - 06:45:38 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.