[phenixbb] molprobity vs validation_cryoem

Roberto Marabini roberto at cnb.csic.es
Fri Apr 26 01:51:48 PDT 2019

Hi guys,

   We are using phenix version 1.15.2-3472. We have executed molprobity
using the command line:

"path_to_pdb"/refmac-refined.pdb pickle=True

We have also executed validation_cryoem (here we have used both the GUI and
the command line and both interfaces return the same result)

"path_to_pdb"/refmac-refined.pdb "path_to_map"/molprobity.mrc
resolution=3.2 pickle=True

What we do not fully understand is why the two commands return different
results for molprobity. Are the default parameters different?

For example, validation_cryoem reports as number of outliers "34" in the
molprobity tab (model.geometry.angle.outliers) while molprobity reports 21

The test files are available at:

pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/

    Thanks for the help
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