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Hi Pavel, <br>
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Thank you. I am actually only interested in getting the MolProbity score. So I ran the phenix.molprobity and it generate a file with the summary table that the MolProbity score is the last line of the file. I guess I will have to extract that line from the
output files for comparison. I am not sure whether there is a simpler way to get the information.
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Best. <br>
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Jing<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Friday, May 15, 2020 12:08 PM<br>
<b>To:</b> Jing Liu <jliu321@stanford.edu>; phenixbb@phenix-online.org <phenixbb@phenix-online.org><br>
<b>Subject:</b> Re: [phenixbb] Is there a way to evaluate batch pdb models with Malprobity in phenix?</font>
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<div>Hi Jing,<br>
<br>
it depends what exactly statistics you want to get. Running<br>
<br>
phenix.model_statistics model.pdb<br>
<br>
will likely get you most you want to see, a sample output looks like:<br>
<br>
<tt>Deviations from Ideal Values.</tt><tt><br>
</tt><tt> Bond : 0.008 0.054 992</tt><tt><br>
</tt><tt> Angle : 1.071 6.317 1346</tt><tt><br>
</tt><tt> Chirality : 0.063 0.191 143</tt><tt><br>
</tt><tt> Planarity : 0.007 0.050 177</tt><tt><br>
</tt><tt> Dihedral : 27.365 179.733 369</tt><tt><br>
</tt><tt> Min Nonbonded Distance : 2.116</tt><tt><br>
</tt><tt><br>
</tt><tt>Molprobity Statistics.</tt><tt><br>
</tt><tt> All-atom Clashscore : 2.62</tt><tt><br>
</tt><tt> Ramachandran Plot:</tt><tt><br>
</tt><tt> Outliers : 0.81 %</tt><tt><br>
</tt><tt> Allowed : 6.50 %</tt><tt><br>
</tt><tt> Favored : 92.68 %</tt><tt><br>
</tt><tt> Rotamer Outliers : 2.91 %</tt><tt><br>
</tt><tt> Cbeta Deviations : 0.00 %</tt><tt><br>
</tt><tt> Peptide Plane:</tt><tt><br>
</tt><tt> Cis-proline : 0.00 %</tt><tt><br>
</tt><tt> Cis-general : 0.00 %</tt><tt><br>
</tt><tt> Twisted Proline : 0.00 %</tt><tt><br>
</tt><tt> Twisted General : 0.00 %</tt><tt><br>
</tt><tt><br>
</tt><tt>Rama-Z (Ramachandran plot Z-score):</tt><tt><br>
</tt><tt>Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.</tt><tt><br>
</tt><tt>Scores for whole/helix/sheet/loop are scaled independently;</tt><tt><br>
</tt><tt>therefore, the values are not related in a simple manner.</tt><tt><br>
</tt><tt> whole: -1.36 (0.65), residues: 123</tt><tt><br>
</tt><tt> helix: -1.04 (0.99), residues: 10</tt><tt><br>
</tt><tt> sheet: 0.56 (1.03), residues: 21</tt><tt><br>
</tt><tt> loop : -1.34 (0.57), residues: 92</tt><tt><br>
</tt><br>
In expect way you can put together a Python script and that would loop over models, get an object-container from calling model_statistics and programmatically parse that object to extract information you need.<br>
<br>
Pavel<br>
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<div class="x_moz-cite-prefix">On 5/15/20 11:54, Jing Liu wrote:<br>
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Hi, <br>
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I had generate a batch of pdb models (40-100) in rosetta and am wondering whether there is a way to evaluate these models in batch with Molprobity. For example, can I use phenix command line to do it and how? Or should I download the Molprobity and do it on
my local computer? Really appreciate if anyone can share their experience.</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Jing Liu, PhD <br>
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Ted Jardetzky lab <br>
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Department of Structural Biology <br>
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Stanford University <br>
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