[phenixbb] cif_as_mtz assertion error

Eric Williams ericwilliams at pobox.com
Wed Jun 13 09:20:16 PDT 2012

The work-around seems to work...er...around. Thanks. :)


On Wed, Jun 13, 2012 at 11:17 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Wed, Jun 13, 2012 at 8:05 AM, Eric Williams <ericwilliams at pobox.com>
> wrote:
> > 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
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