[phenixbb] Geometry analysis

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Apr 29 09:02:59 PDT 2009

Hi Ulrich,

> I am just wondering whether there is a tool/feature in Phenix
> that (i) prints out all bonds/angles deviating by some specified
> number of standard deviations, and (ii) reads a user-defined .cif
> file for ligands as well so that this ligand appears in (i) as
> well. Phenix.pdbtools prints a bond histogram and I did not manage
> to include an external .cif file.

You can just add the .cif files to the phenix.pdbtools command line.
However, phenix.pdbtools will not give you the info you want.

You can use phenix.refine:

  phenix.refine --dry-run your.mtz your.pdb your.cif

Then look at the .geo file, which lists all the restraints. It will
be best to use a recent nightly build, because then the restraints
are conveniently sorted in the .geo file.

The phenix.refine output / .log shows a subset of the info in the
.geo file.

If you don't have an mtz file, you can quickly make one like this:

  iotbx.pdb.as_xray_structure your.pdb --fake=3

Sorry for the contortions. We'll add something simpler to the GUI or
phenix.pdbtools when we get a chance.


P.S.: https://www.phenix-online.org/download/nightly_builds.cgi

Multiple phenix installations can co-exist. Simply source the
phenix_env of the installation you want to use.

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