Good Morning, 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... With regards, Anna Makal
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
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
Hello,
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.
In case of isotropic atoms it's just |Bi-Bj|, where i and j are indices of bonded atoms, B are their isotropic B-factors. Often one considers <|Bi-Bj|>, where <> is average over all such pairs (or selected atoms), and I would expect as many opinions about what these values should be as many people are aware of such metric. In case of anisotropic atoms the formula is the same, but B means projection of anisotropic vibration component onto bond vector i-j. Hirshfeld's paper (Acta Cryst 197?, ?=6..7...8) discusses values for |Bi-Bj|, but it isn't clear whether that is transferable to macromolecules. If memory serves correctly, Dale Tronrud uses tabulated |Bi-Bj| values for various atom types derived from well determined structures as targets for ADP restraints. Some programs explicitly apply it as part of ADP restraints. Pavel
participants (3)
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amakal＠chem.uw.edu.pl -
Nathaniel Echols -
Pavel Afonine