On Wed, Mar 6, 2013 at 3:36 PM, jan
I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this.
phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line: ... Any ideas what I need to do differently?
I didn't realize this command existed - it is probably obsolete. Use phenix.clashscore instead; it will output both the individual clashes and the overall clashscore. The other MolProbity analyses have their own commands too: phenix.ramalyze phenix.rotalyze phenix.cbetadev For my own testing purposes I made a simple wrapper called mmtbx.validation_summary which gives you all of the overall statistics, but nothing else - useful for comparing refinement protocols, but not for telling you exactly what is wrong with each structure. -Nat