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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