VMD-L Mailing List
From: Magnus Andersson (magnus_at_helium.biomol.uci.edu)
Date: Sun Apr 15 2012 - 18:42:21 CDT
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Hi all,
I would like to align my crystal structure with its accompanying electron density surface on my simulation. The simulated system has a different center since I used "Orient" to recenter the protein and membrane before the simulation. Now, all volumetric maps are centered differently compared to the electron density map - you see the problem.
Is there a way I can center the crystal structure AND the electron density map onto the simulated structure? I tried to use "Orient" on the electron density map but that doesn't work.
Perhaps I could get the difference vectors between the structures (by using align) and then apply these vectors on the map. I don't know if this is going to work or how to perform the steps...
Thanks
Magnus Andersson
===================================
Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540
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