[phenixbb] cif_as_mtz assertion error

Nathaniel Echols nechols at lbl.gov
Wed Jun 13 08:17:25 PDT 2012

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:


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


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