[phenixbb] cif_as_mtz assertion error

Pavel Afonine pafonine at lbl.gov
Wed Jun 13 10:02:53 PDT 2012


>     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, 

I will try to find time to update it next week.
Since phenix.cif_as_mtz extracts all data arrays now (thanks Richard!) I 
will have to change my scripts in order to check these arrays to choose 
the one that was actually used to produced the final deposited structure.

>     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.

I wouldn't say it's obsolete, it's just reflects the state as of August 
last year, and that's 50+k entries - good enough for statistical 
exploration. But of course it's not suitable if you want to look at 
recent year-old entries.


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