[phenixbb] molprobity vs validation_cryoem

[Roberto Marabini]

Hi guys,

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

phenix.python_1.15.2-3472
/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/command_line/molprobity.py
"path_to_pdb"/refmac-refined.pdb pickle=True
nproc=4

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

phenix.python_1.15.2-3472
./phenix/phenix/command_line/validation_cryoem.py
"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:

3Dmap:
https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwai04RWxz
pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/

    Thanks for the help
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