VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 01 2008 - 21:54:14 CDT

Hi,
  There's no built-in method for doing a constrained fit like
you describe, but you could presumably hack something together
yourself by "undoing" unwanted rotation components for yourself
by applying the transformation matrix to some reference points
and attempting to decompose the rotation into xy and z components,
keeping only the ones you want. Perhaps someone else has a better
suggestion, but that's all that comes to mind just now.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 01, 2008 at 10:59:04AM +0100, Benjamin Hall wrote:
> Hi
>
> I'm interested in performing an alignment of 2 structures in a
> membrane. Normally I would use the "measure fit..." command as
> described in the manual, but I really want to fit the structures using
> only translation components in x and y and rotation components around
> z, so that the relative positions in the membrane aren't changed by
> the fit (that is, the planes and positions of the membrane in z match
> after the fit, if they matched initially). Is this possible in VMD,
> either through the measure command or by another method?
>
> Many thanks in advance,
>
> Ben
>
>
> ************************************************************************
> Benjamin A. Hall
> Structural Bioinformatics & Computational Biochemistry Unit
> University of Oxford
> http://sbcb.bioch.ox.ac.uk/hall.php
> +44 (0)1865 275380
> benjamin.hall_at_bioch.ox.ac.uk
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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