[phenixbb] Is there a way to evaluate batch pdb models with Malprobity in phenix?
jliu321 at stanford.edu
Mon May 18 16:26:25 PDT 2020
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.
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?
it depends what exactly statistics you want to get. Running
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
All-atom Clashscore : 2.62
Outliers : 0.81 %
Allowed : 6.50 %
Favored : 92.68 %
Rotamer Outliers : 2.91 %
Cbeta Deviations : 0.00 %
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.
On 5/15/20 11:54, Jing Liu wrote:
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
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