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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>
<br>
<div class="moz-cite-prefix">On 5/15/20 11:54, Jing Liu wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BYAPR02MB49847C6893C34794520793D49DBD0@BYAPR02MB4984.namprd02.prod.outlook.com">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hi, <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Jing Liu, PhD <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Ted Jardetzky lab <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Department of Structural Biology <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Stanford University <br>
</div>
<br>
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