quick clashlist or molprobity in batch mode
Hi all, 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: "phenix.quick_clashlist model=mypdb.pdb" ... the output tells me: # run_clashlist # # Run reduce and molprobity # type phenix.run_clashlist: --help for help Parameters used: run_clashlist { model = "4iuj.pdb" build = True summary_file = None output_file = None temp_dir = None remove_temp_dir = None verbose = False raise_sorry = False debug = False dry_run = True } ************************************************ 'str' object has no attribute '_anchor' ************************************************ Any ideas what I need to do differently? thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
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
participants (2)
-
jan -
Nathaniel Echols