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. Ralf 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.