On Feb 22, 2008, at 3:45 AM, Jean-Didier Maréchal wrote:

Hi Guys,

I'd like to superpose two inorganic complexes using two differently "ordered" atom sets. My compound has quite similar substructures but I am sure at all what is the best "ordered" selection of atom pairs to align. Therefore, I'd like to make a "extensive" search (with an heuristic approach to define...) passing by the idle. I am unfortunately missing something before getting to this point!

Lets say that I just want to align the nitrogen atoms of the my two structures. I have:

import chimera import numpy from chimera import match from chimera import runCommand runCommand("select #1@N=") an1=chimera.selection.currentAtoms() runCommand("select #0@N=) an2=chimera.selection.currentAtoms() chimera.match.matchAtoms(an1,an2)

And then it's when I am already stuck!

the resulting prompt does not provide mistake an gives: chimera.match.matchAtoms(an1,an2) (<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358)

But how this results can be send to the graphical window? I guess I have to use the Xform object, but I can not clearly understand how to do this.

Thanks for any help!

JD

Hi JD, I'm not 100% certain what your goal is, but you could just run the match command directly: from chimera import runCommand runCommand("match #1@N= #0@N=") If you need access to the RMSD of the match, you could call the underlying match() function: from Midas import match mobileAtoms, refAtoms, rmsd = match("#0@N=", "#1@N=") which will also superimpose the structures. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu