<div dir="ltr">Thanks for the explanation.<div><br></div><div> roberto</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 26, 2019 at 4:03 PM Oleg Sobolev <<a href="mailto:osobolev@lbl.gov">osobolev@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">Hi Roberto,<div><br></div><div>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</div><div>REMARK 3 CDL<br></div><div>to your pdb file.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 26, 2019 at 6:14 AM Roberto Marabini <<a href="mailto:roberto@cnb.csic.es" target="_blank">roberto@cnb.csic.es</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr">Sorry, In the previous email I sent a wrong link for the pdb file. The rigth one is: </div><div dir="ltr"><br></div><div dir="ltr"><a href="https://drive.google.com/open?id=0B_i_LJfUN1z7dEF6MHhzNEJvUEo2eUJCZmNRYUpfVFFLZy1j" target="_blank">https://drive.google.com/open?id=0B_i_LJfUN1z7dEF6MHhzNEJvUEo2eUJCZmNRYUpfVFFLZy1j</a></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 26, 2019 at 10:51 AM Roberto Marabini <<a href="mailto:roberto@cnb.csic.es" target="_blank">roberto@cnb.csic.es</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><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" target="_blank">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/" target="_blank">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>
</blockquote></div></div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>