[phenixbb] Model_vs_data speed

Oleg Sobolev osobolev at lbl.gov
Mon Oct 16 10:44:08 PDT 2017

Hi Eric,

We will definitely have a look at model_vs_data speed.

In the mean time, if you have some Python skills, you may consider looking
at a Python pickle file in your Phenix distribution:
It contains various statistics (R-factors, etc, more than 70
characteristics) for ~70 000 pdb files. If what you want to obtain from
model_vs_data is present there, you may be able to skip calculations and
get the numbers you want.

If you are interested, I can write a small script illustrating how to get
some numbers.

Best regards,
Oleg Sobolev.

On Sun, Oct 15, 2017 at 10:10 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Eric,
> I'm sorry it is slow, or slower than you expect. I'm sure technically it
> can run up to 10 seconds max per largest structure in PDB, as advertised in
> http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf
> if corresponding code is appropriately refactored (making most use of
> above paper); plus time taken by phenix.molprobity.
> Unfortunately, I'm away till October 26, and then will be at the workshop
> till November 6th.
> Others from the team (Dorothee, Oleg, Nigel, Billy, Vincent, Chris?) are
> encouraged to feel free to volunteer to address obvious runtime bottlenecks
> in this code.
> All the best,
> Pavel
> On 10/15/17 04:35, Eric Williams wrote:
> I'm having a devil of a time getting model_vs_data to run in a timely
> fashion. Running the latest stable Linux build on Ubuntu 14.04 takes on the
> order of 3 minutes per structure. That wouldn't be so bad if I weren't
> trying to run it on every entry in the PDB. Is it just a limitation of
> Python? SFCheck, which I think is written mostly in FORTRAN, runs in a few
> seconds. Any help anyone could offer would be appreciated. Thanks. :)
> Eric
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