Daniel,
first, it's important to have the two brackets without whitespace:
[[
not
[ [
I know, why should that be, right? ....
second, for rotateSelected you need to indicate that you want a MOLECULAR
rotation, not one that is defined by the window.
The code is:
r = [[ 0.49441794888, 0.6513774372, -0.5755504549 ], [0.68161107155,
-0.70143415565, -0.20831819995 ], [
-0.53940452257,-0.28930530516, -0.79078770946 ]]
rq = quaternion(r)
t = { 24.48061828, 16.111736935, 99.953849304 }
rotateSelected MOLECULAR @rq
translateSelected @t
On Mon, Dec 21, 2009 at 10:25 AM, Daniel Lundin
<[email protected]>wrote:
> Hi,
>
> I'm new to the list, but have searched the net for a couple of days for
> hints as to solve the below described problem, but to no avail. In
> brief, I have plenty of rotation matrices and translation vectors mainly
> from EBI's SSM service, but also from the Dali protein structure
> aligner. What I'd like to do is take any pair of structures, look up the
> rotation matrix and translation vector for the target structure and view
> the query and target superposed in Jmol. After reading what I could find
> about quaternions, I have tried the approach below (which is SSM data,
> but Dali matrices/vectors fail also), but the second structure ends up
> far away from the first. Whether it's rotated correctly or not, I don't
> know for sure, but it seems to be close at least. The loaded structure
> files are straight from PDB.
>
> $ show _version
> _version = 1109011
> $ load 1mxr.pdb
> $ select *
> $ cpk off
> $ wireframe off
> $ select :A
> $ cartoon
> $ colour blue
> $ appendNew=true
> $ load append 1afr.pdb
> $ frame *
> $ select */2
> $ cpk off
> $ wireframe off
> $ select :C/2
> $ cartoon
> $ colour red
> $ r = [ [ 0.49441794888, 0.6513774372, -0.5755504549 ], [
> 0.68161107155, -0.70143415565, -0.20831819995 ], [ -0.53940452257,
> -0.28930530516, -0.79078770946 ] ]
> $ rq = quaternion(r.col(1), r.col(2))
> $ t = { 24.48061828, 16.111736935, 99.953849304 }
> $ rotateSelected @rq
> $ translateSelected @t
>
> I have also tried applying the matrix/vector to the first (query)
> structure. Does anyone know what the problem is?
>
> /D
>
> --
> Daniel Lundin
>
> Department of Molecular Biology & Functional Genomics
> Arrhenius Laboratories for Natural Sciences
> Stockholm University, SE-106 91 Stockholm, Sweden
>
> tel. +46 (0)8 16 41 95, mobile: +46 (0)708 123 922, fax. +46 (0)8 16 64 88
>
> Email: [email protected]
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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