Hi Engin, that's right, it outputs only global figures... Tools that Nat listed output detailed lists. Pavel On 5/1/13 12:26 PM, Engin Özkan wrote:
Thanks Pavel. This does half the job by reporting the overall values, but does not list detail. For example, it tells you the Ramachandran outlier percentage, but does not list the outlier residues. Or the bond and angle outliers. I would like to see those output as well. These are all done beautifully in the GUI, but apparently not output as human-readable text files.
I looked at full parameter list, but could not see a longer output switch.
Engin
On 5/1/13 12:19 PM, Pavel Afonine wrote:
Hi Engin,
try:
phenix.pdbtools model_stat=true model.pdb
If this doesn't do what you want then please let me know.
Pavel
On 5/1/13 12:15 PM, Engin Özkan wrote:
Hi everybody,
I want to create a comprehensive, human-readable log file by running validation using molprobity tools within phenix command-line. I do not have structure factors/maps. Apparently, the GUI runs validation through phenix.model_vs_data (according to the .eff file), but in command-line, I cannot get phenix.model_vs_data to run without an mtz/hkl. I guess I could provide it a fake data file, and then set the comprehensive flag to "True"? BTW, the log file produced by the GUI is not comprehensive at all.
I could not find a related mmtbx or cctbx function either. Another mentioned tool, phenix.validate, does not even exist in my installation (dev 1361).
Thanks, Engin
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