Hi Pavel, Did you find time to modify phenix.validation_cryoem ? thanks for the help Roberto On Wed, Mar 6, 2019 at 3:47 PM Pavel Afonine wrote:

Hi Roberto,

I don't think we have it. I will double-check now. If we don't have it I will add it today so that it's available in tomorrow's build.

Pavel

On 3/6/19 06:25, Roberto Marabini wrote:

...

Hi,

I see that it is possible to execute phenix.validation from command line by typing:

phenix.validation_cryoem <path to>/5ni1.cif <path to>/molprobity.mrc resolution=2.2

The program runs smoothly and prints on screen a few hundreds of lines. The more or less equivalent program in version 1.13 was phenix.molprobity, when executed with the option pickle=True, phenix.molprobity saved to the hard-disk a pkl file containing all data.

Is there an equivalent flag for phenix.validation_cryoem? where is the result of executing this shell being saved?

thanks

Roberto

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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 week. -- 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 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I see that in phenix 1.14 (and 1.15) the command phenix.molprobity has been replaced by the more general phenix.validation_cryoem.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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]