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 *Sent:* Friday, May 15, 2020 12:08 PM *To:* Jing Liu ; [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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