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

Pavel Afonine pafonine at lbl.gov
Mon May 18 17:51:51 PDT 2020

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 <pafonine at lbl.gov>
> *Sent:* Friday, May 15, 2020 12:08 PM
> *To:* Jing Liu <jliu321 at stanford.edu>; phenixbb at phenix-online.org
> <phenixbb at phenix-online.org>
> *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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