[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 


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