Magnus, With a little effort and the qkabsch.py file from the CEalign package you can do this. It would take a little bit of programming, but you'd only have to modify one line, I think.
IIRC, all you have to do is create the vector of weights and then multiply that by the paired vectors making the correlation matrix. In the function simplAlign (line 123 from qkabsch.py) there is: V, S, Wt = numpy.linalg.svd(numpy.dot(numpy.transpose(mat2), mat1)) where I think you could get away with something like V, S, Wt = numpy.linalg.svd(numpy.dot(numpy.transpose(numpy.dot(W,mat2)), mat1)) where W is your weight vector. You can get the CEAlign package from the PyMOLWiki: http://www.pymolwiki.org/index.php/Cealign and learn more about the problem, from a great write-up, here, http://boscoh.com/protein/rmsd-root-mean-square-deviation HTH, -- Jason > From: Magnus Franzmann [mailto:m...@bio.aau.dk] > Sent: Monday, January 19, 2009 5:00 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] weighted alignment > > > > Dear all > > > > I would like to perform an alignment of two molecules with parts of the > molecules weighted differently. Is this possible in pymol? > > > > Best regards > > Magnus Franzmann -- Jason Vertrees, PhD Dartmouth College : j...@cs.dartmouth.edu Boston University : jas...@bu.edu PyMOLWiki : http://www.pymolwiki.org/
