[phenixbb] quick clashlist or molprobity in batch mode

Nathaniel Echols nechols at lbl.gov
Wed Mar 6 15:44:29 PST 2013

On Wed, Mar 6, 2013 at 3:36 PM, jan <jan.abendroth at gmail.com> wrote:
> I want to analyze a whole bunch of structures with molprobity, and I am
> looking for a convenient way to do this.
> phenix.quick_clashlist seems to be a handy tool. However, when I use the
> following command line:
> ...
> Any ideas what I need to do differently?

I didn't realize this command existed - it is probably obsolete.  Use
phenix.clashscore instead; it will output both the individual clashes
and the overall clashscore.

The other MolProbity analyses have their own commands too:


For my own testing purposes I made a simple wrapper called
mmtbx.validation_summary which gives you all of the overall
statistics, but nothing else - useful for comparing refinement
protocols, but not for telling you exactly what is wrong with each


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