[phenixbb] advice for speeding up cif_as_mtz

Eric Williams ericwilliams at pobox.com
Mon Sep 10 12:31:48 PDT 2012

I'm running it on a CIFS-mounted disk. Phenix and the data are located on
the same disk, though.

I'll give a newer build a try. Thanks. :)


On Mon, Sep 10, 2012 at 3:20 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Mon, Sep 10, 2012 at 7:38 AM, Eric Williams <ericwilliams at pobox.com>
> wrote:
> > 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).
> >
> > 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>
> >
> > I'm hoping that perhaps someone could help me determine which command
> line
> > argument(s) could be removed to provide maximum speed-up.
> Are you running this on NFS-mounted disks by any chance?
> None of these should be especially time-consuming - the only big
> bottleneck in the program is "--use-model".  I just tried running the
> command above on a reasonably large structure (1zy8) and it was very
> quick (< 15s).  On the off chance that something big changed in the
> last couple of weeks, can you update to the latest nightly build and
> see if it's still running slowly?  If so, send us some IDs that take a
> particularly long time and we'll see if we can reproduce the problem.
> thanks,
> Nat
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