[phenixbb] Hirshfeld (rigid bond) test
amakal at chem.uw.edu.pl
amakal at chem.uw.edu.pl
Thu Jan 31 02:42:05 PST 2013
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
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