Re: [phenixbb] advice for speeding up cif_as_mtz

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. :) Eric On Mon, Sep 10, 2012 at 3:20 PM, Nathaniel Echols wrote:

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I'm currently running cif_as_mtz and model_vs_data on the whole PDB as

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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 --ignore-bad-sigmas --merge --remove-systematic-absences --map-to-asu --symmetry= --output-file-name=

I'm hoping that perhaps someone could help me determine which command

On Mon, Sep 10, 2012 at 7:38 AM, Eric Williams wrote: part line

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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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb