<div dir="ltr">Thanks!<div><br></div><div>I used the bash scripts you two provided. It works great. </div><div><br></div><div>A further question, how do I extract the output summary of the molprobity results from all 100 files into a single file. Ideally, I would like to make the data into a table. </div><div><br></div><div>Appreciate your help!</div><div><br></div><div><div>=================================== Summary ===================================</div><div><br></div><div> Ramachandran outliers = 0.38 %</div><div> favored = 95.27 %</div><div> Rotamer outliers = 0.00 %</div><div> C-beta deviations = 10</div><div> Clashscore = 184.98</div><div> RMS(bonds) = 0.0193</div><div> RMS(angles) = 2.77</div><div> MolProbity score = 3.06</div></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Jun 25, 2018 at 5:32 PM Oleg Sobolev <<a href="mailto:osobolev@lbl.gov">osobolev@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Charles,<div><br></div><div>I would use any scripting language you are familiar with - python, bash, csh. Here is a bash script adapted from</div><div><a href="https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory" target="_blank">https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory</a><br></div><br><div><div>for file in *.pdb</div><div>do</div><div> echo $file</div><div> phenix.molprobity "$file" > "$file"_results.txt</div><div>done</div></div><div><br></div><div>On mac - make a file mpscript put it in a directory with your .pdb, then run</div><div>chmod a+x mpscript</div><div>./mpscript</div><div><br></div><div>Hope it helps.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 25, 2018 at 1:39 PM, CPMAS Chen <span dir="ltr"><<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, All,<div><br></div><div>I have about 100 structures needs be validated and optimized. what will be a fast way to do so? Can I somehow put phenix.molprobity in a circle?<br clear="all"><div><br></div><div>Thanks!</div><div><br></div>-- <br><div dir="ltr" class="m_7869143088461595327m_674535493315817815gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>
<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Instructor</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p><p></p></div></div></div></div></div>
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<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Instructor</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p><p></p></div></div></div>