VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 17 2012 - 00:13:31 CDT
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Hi,
I've forwarded your note to one of the MDFF developers as I'm sure
he can give you some helpful tips.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Sun, Apr 15, 2012 at 04:42:21PM -0700, Magnus Andersson wrote:
> 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
> ===================================
>
>
>
>
>
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
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- In reply to: Magnus Andersson: "align electron density map onto simulated structure (with different center)"
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