[phenixbb] Fwd: running phenix.validation from command line

Billy Poon BKPoon at lbl.gov
Mon Apr 8 15:17:57 PDT 2019

Hi Roberto,

I checked in basic functionality so that adding "pickle=True" to the
command line will dump the same results object that the GUI uses for
displaying the data. The filename is currently hard-coded as
"validation_cryoem.pkl" and that file will be overwritten without warning,
but I'll be adding more functionality to make it more user friendly.

The feature will be available in the next build that will be released this

Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Mon, Apr 8, 2019 at 7:22 AM Roberto Marabini <roberto at cnb.csic.es> wrote:

> Hi,
>    I see that in phenix 1.14 (and 1.15) the command phenix.molprobity has
> been replaced by the more general  phenix.validation_cryoem. In the old
> version (1.13) phenix.molprobity, when executed with the
> option pickle=True,  saved to the hard-disk a pkl file containing all data.
> Is there an equivalent flag for phenix.validation_cryoem? I asked this
> question a  month ago and I understood from the answer that the option was
> not available but that you plan to incorporate it.    Did you find time
> modify phenix.validation_cryoem ?
>    thanks
>   Roberto
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