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 a11-a33 are the matrix elements (check whether they have to be
transposed) and d1-d3 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 <pa...@cornell.edu> 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 least-squares superimposition of STRID2 (X)
onto STRID1
>> NR. STRID1 STRID2 U(.,1) U(.,2) U(.,
>> 3) T(.)
>> 1: 9506-A 1ris U(1,.) -0.230692 -0.010007
>> -0.972975 50.701385
>> 1: 9506-A 1ris U(2,.) 0.443459 0.888979
>> -0.114287 31.716473
>> 1: 9506-A 1ris U(3,.) 0.866098 -0.457839
>> -0.200643 26.479412
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
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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
