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