Hi Nat, thank you for responding. I am looking forward to the next build.
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.
I guess it is not terribly useful in most cases, but it would be a valuable tool for comparing the outcomes of different refinement strategies for the same macromolecule, especially as rigid-bond-test, unlike ADP values, should be in principle independent from effects of different anisotropic scaling factors. Averaging rigid-bond-test values over domains, main chain/side chain of a certain residue, or over certain bond-types (peptide, C-Cring a.s.o) would be a nice validation tool too.
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.
I am not terribly familiar with PyMOL, but I think that coloring bonds by the actual rigid-bond-test value would be just great - I guess I would have to think about it too. With regards, Anna Makal