Hi Jing,

so then it looks like the problem solved! Perhaps that's the simplest way though may not be most efficient as phenix.molprobity calculates a lot more that you don't use. More efficient would be to write your own Python script to loop over files and get that number directly in the script..

Pavel

On 5/18/20 16:26, Jing Liu wrote:
Hi Pavel,

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.

Best.

Jing
From: Pavel Afonine <[email protected]>
Sent: Friday, May 15, 2020 12:08 PM
To: Jing Liu <[email protected]>; [email protected] <[email protected]>
Subject: Re: [phenixbb] Is there a way to evaluate batch pdb models with Malprobity in phenix?
�
Hi Jing,

it depends what exactly� statistics you want to get. Running

phenix.model_statistics model.pdb

will likely get you most you want to see, a sample output looks like:

Deviations from Ideal Values.
� Bond����� :� 0.008�� 0.054��� 992
� Angle���� :� 1.071�� 6.317�� 1346
� Chirality :� 0.063�� 0.191��� 143
� Planarity :� 0.007�� 0.050��� 177
� Dihedral� : 27.365 179.733��� 369
� Min Nonbonded Distance : 2.116

Molprobity Statistics.
� All-atom Clashscore : 2.62
� Ramachandran Plot:
��� Outliers :� 0.81 %
��� Allowed� :� 6.50 %
��� Favored� : 92.68 %
� Rotamer Outliers :� 2.91 %
� Cbeta Deviations :� 0.00 %
� Peptide Plane:
��� Cis-proline���� : 0.00 %
��� Cis-general���� : 0.00 %
��� Twisted Proline : 0.00 %
��� Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
� whole: -1.36 (0.65), residues: 123
� helix: -1.04 (0.99), residues: 10
� sheet:� 0.56 (1.03), residues: 21
� loop : -1.34 (0.57), residues: 92

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.

Pavel

On 5/15/20 11:54, Jing Liu wrote:
Hi,

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.

Jing Liu, PhD
Ted Jardetzky lab
Department of Structural Biology
Stanford University 

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