[phenixbb] Hirshfeld (rigid bond) test

Nathaniel Echols nechols at lbl.gov
Wed Jan 30 14:47:27 PST 2013

On Tue, Jan 29, 2013 at 3:51 AM,  <amakal at chem.uw.edu.pl> wrote:
> 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.


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