[phenixbb] advice for speeding up cif_as_mtz

Pavel Afonine pafonine at lbl.gov
Wed Sep 19 10:36:54 PDT 2012


Hi Eric,

I just tried this command:

phenix.cif_as_mtz 3a0n-sf.cif --ignore-bad-sigmas --merge 
--remove-systematic-absences --map-to-asu --symmetry=3a0n.pdb

and it tool approximately 5 seconds to run on my computer.

Pavel

On 9/18/12 4:53 PM, Eric Williams wrote:
> It seems that the location of Phenix does matter (at least on my 
> system). I ran cif_as_mtz (from 1.8.1-1155) on 3a0n, using only the 
> "--merge" switch. Running from the CIFS mount, it took ~5 minutes. 
> Running from the local file system, it took ~21 seconds. The CIF file 
> was on the local file system in both experiments.
>
> Weird.
>
> Eric
>
> On Mon, Sep 10, 2012 at 3:51 PM, Nathaniel Echols <nechols at lbl.gov 
> <mailto:nechols at lbl.gov>> wrote:
>
>     On Mon, Sep 10, 2012 at 12:31 PM, Eric Williams
>     <ericwilliams at pobox.com <mailto:ericwilliams at pobox.com>> wrote:
>     > I'm running it on a CIFS-mounted disk. Phenix and the data are
>     located on
>     > the same disk, though.
>
>     It doesn't matter where Phenix is - the IO overhead from reading the
>     CIF and writing the MTZ could be substantial though.  Try running a
>     few jobs with files on a local disk and see if that goes faster.
>
>     -Nat
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>
>
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