<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hi guys,</div><div><br></div><div> We are using phenix version 1.15.2-3472. We have executed molprobity using the command line:</div><div><br></div><div>phenix.python_1.15.2-3472 <br>
/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/command_line/molprobity.py "path_to_pdb"/refmac-refined.pdb pickle=True <br>
nproc=4</div><div><br></div><div>We have also executed validation_cryoem (here we have used both the GUI and the command line and both interfaces return the same result)<br></div><div><br></div><div>phenix.python_1.15.2-3472 <br>
./phenix/phenix/command_line/validation_cryoem.py <br>
"path_to_pdb"/refmac-refined.pdb "path_to_map"/molprobity.mrc <br>
resolution=3.2 pickle=True</div><div><br></div><div>What we do not fully understand is why the two commands return different results for molprobity. Are the default parameters different? <br></div><div><br></div><div>For example, validation_cryoem reports as number of outliers "34" in the molprobity tab (model.geometry.angle.outliers) while molprobity reports 21<br></div><div><br></div><div>The test files are available at:</div><div><br></div><div>3Dmap: <a href="https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwai04RWxz">https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwai04RWxz</a><br></div><div>pdb file: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/</a></div><div><br></div><div> Thanks for the help<br></div></div></div></div></div>