Thanks for the explanation. roberto On Fri, Apr 26, 2019 at 4:03 PM Oleg Sobolev wrote:

Hi Roberto,

The difference occurs because of using/not using CDL (conformation-dependent library) modifications. In case of molprobity, CDL is not used since it is not mentioned the pdb file header which lead us to assume that it was refined without CDL. In case of cryoem_validation it is used. To turn it off use "cdl=False" command-line parameter or locate this flag in GUI. To turn it on for molprobity, add line REMARK 3 CDL to your pdb file.

Best regards, Oleg Sobolev.

On Fri, Apr 26, 2019 at 6:14 AM Roberto Marabini wrote:

...

Sorry, In the previous email I sent a wrong link for the pdb file. The rigth one is:

https://drive.google.com/open?id=0B_i_LJfUN1z7dEF6MHhzNEJvUEo2eUJCZmNRYUpfVF...

On Fri, Apr 26, 2019 at 10:51 AM Roberto Marabini wrote:

...

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_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwai... pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/

Thanks for the help

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