On Mon, Dec 21, 2009 at 1:43 PM, Daniel Lundin
<[email protected]>wrote:
> Robert Hanson skrev:
>
> Thanks a lot for your quick reply.
>
> > Daniel,
> >
> > first, it's important to have the two brackets without whitespace:
> >
> > [[
> >
> > not
> >
> > [ [
> >
> > I know, why should that be, right? ....
> >
> Well, I don't have a clue ;-) And whitespace seems to work fine...
>
>
(I was wrong about that --- nevermind!)
> (On a similar note, I must confess that I don't really understand why
> one should sometimes use straight brackets and othertimes curly, though
> I'm guessing that the former is for matrices, while the other's for
> vectors.)
>
>
yeah, that's a bit tricky. { } are used for several things.
Could be a point or vector {x y z},
x = {1.0 3.0 2.0}
could be a quaternion:
$ show orientation rotation
{0.74129415 0.006376769 -0.33657235 0.580656}
could be a set of atoms if in a math context:
$ print {*/2.1}
({6461:23786})
$ select {*/2.1}
17,326 atoms selected
after an '@' it is a math expression embedded in a standard command:
load @{"c:/temp/" + filename}
Pretty much unambiguous.
> Nice that one doesn't need the r.col(1), r.col(2) construct I found in a
> quite recent list discussion. It made me nervous that I was throwing
> away something.
>
>
The rotational matrix only needs 6 elements; the others are redundant.
The columns of the vectors are the transformed X, Y, and Z vectors, so
if you have two you can always get the third.
> > t = { 24.48061828, 16.111736935, 99.953849304 }
> > rotateSelected MOLECULAR @rq
> > translateSelected @t
> >
> Thanks a lot, that works perfectly.
>
>
Oh, good!
> /Daniel
> >
> >
> > 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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> >
> >
> >
> >
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>
> --
> 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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