Hi Jan, there is no dedicated tool that would do it in one go, but I think you can put something together from pieces scattered across cctbx and phenix code. Oh and by the way I don't know what is "direct space atomic distances "... First I would superpose two structures using a call like this (copied from phenix/phenix/command_line): from scitbx.math import superpose superpose.least_squares_fit(reference_sites = fixed_sites, other_sites = moving_sites) rmsd = fixed_sites.rms_difference(moving_sites) this assumes structures are aligned. Then just loop over bonds and collect bond distances into flex double array and then compute call .min_max_mean()... Pavel On 3/4/13 4:06 AM, Jan Marten Simons wrote:
Hi,
I think I've seen some code in cctbx which tries to put the similarity of two crystal structures into a number. Am I right on this?
I want to have something similar:
I'm interested in comparing the direct space atomic distances of two structures sharing the same unit cell parameters and space group and scatterers but different atomic coordinates for those. Now I'd like to have a mapping where I could compare the bond lengths between all scatterers which should eliminate any movements which might also be due to a shift in the origin of a P 1 cell. Also I'd like to have a value for mean, minimal and maximal displacements. The purpose of this is to check how good a structure approximation matches a reference structure.
How would you suggest to take on this task? Or is there even some code related to this?
Thanks in advance,
Jan _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb