Re: [phenixbb] Is there a way to evaluate batch pdb models with Malprobity in phenix?

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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