Hi,
You can do this using alter_state:
alter_state 1,selection,(x,y,z) =
(a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2,
a31*x+a32*y+a33*z+d3)
where a11a33 are the matrix elements (check whether they have to be
transposed) and d1d3 are the elements of the shift vector.
It may be convenient to make this a function which you can load at
startup time (especially if you have to do this many times). For
example, paste the following in a file mtransform.py:
from pymol import cmd
def mtransform( selection="all", matrix=[[1,0,0],[0,1,0],[0,0,1],[0,0,0]] ):
if ( len(matrix) == 3 ): # In this way it is also valid to give a
3x3 matrix for rotation only
matrix.append( [0,0,0] )
a11, a12, a13 = matrix[0][0], matrix[0][1], matrix[0][2]
a21, a22, a23 = matrix[1][0], matrix[1][1], matrix[1][2]
a31, a32, a33 = matrix[2][0], matrix[2][1], matrix[2][2]
d1, d2, d3 = matrix[0][0], matrix[0][1], matrix[0][2]
cmd.alter_state( 1, selection, "(x,y,z) = (%f*x+%f*y+%f*z+%f,
%f*x+%f*y+%f*z+%f, %f*x+%f*y+%f*z+%f )" %
(a11,a12,a13,d1,a21,a22,a23,d2,a31,a32,a33,d3)
#============
Of course it could be done more efficiently, better looking, but that
is left as an exercise for the reader ;) (Think of changing
coordinates directly, adding an option to make a copy of the selection
first, and parse a string for the matrix, such that you can use
cmd.extend and can run the command using:
mtransform all, [[0,1,0],[1,0,0],[0,0,1],[3,1,2]]
rather than:
mtransform("all", [[0,1,0],[1,0,0],[0,0,1],[3,1,2]])
which is the way to invoke the command with the given code.
Hope this helps,
Tsjerk
On 6/30/06, Peter Adrian Meyer <pam52@...> wrote:
> The easiest way I'm aware of to do this would be to use the ccp4 program
> pdbset, but there are numerous other ways/programs that will do this (if
> pymol has this capacity, I'm not aware of it; but someone else will
> correct me).
>
> Pete
>
> <snip>
>
> >> I've been looking through the PyMol reference and wiki page and I can't
> find a command for moving a molecule through a matrix, I
> >> would like to move one pdb onto the other using the info below. Is
> there such a command?
> >> ## MATRICES: UX+T is the leastsquares superimposition of STRID2 (X)
> onto STRID1
> >> NR. STRID1 STRID2 U(.,1) U(.,2) U(.,
> >> 3) T(.)
> >> 1: 9506A 1ris U(1,.) 0.230692 0.010007
> >> 0.972975 50.701385
> >> 1: 9506A 1ris U(2,.) 0.443459 0.888979
> >> 0.114287 31.716473
> >> 1: 9506A 1ris U(3,.) 0.866098 0.457839
> >> 0.200643 26.479412
>
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>
>
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with preintegrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.asus.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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>

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
