On Tue, Jan 29, 2013 at 3:51 AM,
I have a question concering ADP-s analysis and validation. Thanks to the recent discussion on this list I learned about the tools for general ADP-s statistics and average B-factor plotting in PHENIX. Has anyone ever tried to similarly document/visualize the values of the Hirshfeld's rigid bond test for macromolecules, using phenix/cctbx tools?
I know the Hirshfeld's can be calculated during phenix refinement (there is this rigid_bond_test keyword), but I would like to analyze the values for the final model...
We certainly have the ability to do this easily, and I would like to add more analysis features to the GUI anyway, but it's not clear to me how to present the results for a macromolecule. I threw together a script to expose these functions, which I'll call "mmtbx.rigid_bond_test" (it will be in the next build - I can also send you the script but I had to change another file as well). The output looks like this: =============================== Rigid-bond test =============================== pdb=" N LEU A 4 " pdb=" CA LEU A 4 " 24.957 pdb=" CA LEU A 4 " pdb=" C LEU A 4 " 61.442 pdb=" CA LEU A 4 " pdb=" CB LEU A 4 " 19.558 pdb=" C LEU A 4 " pdb=" O LEU A 4 " 75.078 pdb=" C LEU A 4 " pdb=" N THR A 5 " 112.578 ...and so on, but that doesn't seem terribly useful to me by itself. It would be nice if there was a way to visualize this in PyMOL but I'd have to think a little more about how to do that. -Nat