VMD-L Mailing List

From: Benjamin Hall (benjamin.hall_at_bioch.ox.ac.uk)
Date: Thu May 01 2008 - 04:59:04 CDT

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

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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