[phenixbb] advice for speeding up cif_as_mtz
Pavel Afonine
pafonine at lbl.gov
Tue Sep 11 11:38:28 PDT 2012
Hi Eric,
> I'm currently running cif_as_mtz and model_vs_data on the whole PDB as
> part of my dissertation. Time has become a critical concern, and
> cif_as_mtz (dev-1141) is running very, very slowly (1-4 minutes per
> entry).
clearly something is wrong, as the command you quoted should take from
few to ~10-30 seconds, not minutes.
> Here's how I'm calling it:
>
> phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge
> --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn>
> --output-file-name=<sf_mtz_fn>
Clearly I missed a moment when "--ignore-bad-sigmas" was added,
otherwise I would pick up on this earlier. What is the definition of
"bad-sigmas"?
Thanks,
Pavel
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