On Wed, Jun 13, 2012 at 8:05 AM, Eric Williams
How might I know which structures do and don't require --use-model? I'm running cif_as_mtz on the whole PDB so I can then run model_vs_data. If I know when to use that switch and when not to, I can mend my script accordingly.
Pavel might know this, since he's the person who normally runs this. Normally, I would also suggest that you take advantage of a resource in Phenix: $PHENIX/chem_data/polygon_data/all_mvd.pickle which contains model_vs_data results for all applicable PDB entries. However, this has not been updated since at least last August, and in the meantime, there have been thousands of new entries added to the PDB, plus Pavel recently changed the bulk solvent correction and scaling procedure, which tends to result in slightly lower R-factors, so I think it's officially obsolete right now. As it happens, phenix.cif_as_mtz appears to offer an additional way around the crash, which is the argument "--remove_systematic_absences". Try adding this to your existing script (keeping "--use_model") and see if that fixes the problem. Just to be safe, I would also add "--map_to_asu" (which will move reflections around so the h,k,l indices are in the canonical setting) and "--merge" (which will merge non-unique reflections - keeping Friedel pairs separate, of course). Looks like we need to update our documentation. -Nat