Thanks Nigel!
From: Nigel Moriarty
Date: Thursday, September 25, 2025 at 11:37 AM
To: Kevin M Jude
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] inconsistency of Molprobity results between RealSpaceRefine and ValidationCryoEM
Kevin
All of this arises from a simple miscommunication. The default restraints for refinement in Phenix is the Conformation Dependent Library. It basically changes the ideal values for the protein backbone based on the phi/psi.angles. While Moprobity in Phenix uses the same libraries, it appears the communication has broken so it's not using the CDL but rather the single value restraints. As a result, .geo file (which is the gold standard) is correct and the Molprobity is slightly wrong. As a power user (you look in the .geo file), I suggest you check the .geo file until I correct this.
Cheers
Nigel
---
Nigel W. Moriarty
Building 91, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web : CCI.LBL.govhttp://CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464https://orcid.org/0000-0001-8857-9464
On Tue, Sep 23, 2025 at 12:20 PM Kevin M Jude mailto:[email protected]> wrote:
I notice inconsistencies in the Molprobity results reported for the same structure from RealSpaceRefine and from ValidationCryoEM. As an example, for bond angle restraints, RSR reports that there are four >4sigma outliers (but does not list the outliers), while ValidationCryoEM reports 0.
RSR
CryoEMValidation
Number of restraints
13228
13228
RMS(deviation)
0.509
0.51
Max. deviation
9.997
9.998
Min. deviation
0
0
Number of outliers > 4sigma
4
0
Browsing through the .geo file, I don’t see any >4 sigma deviations among the highest residual angles, so I think this is an error.
I also see small discrepancies in Ramachandran favored, rotamer outliers, and clash score which seem to come down to minuscule differences in measurements at the margins.
This is for Phenix 1.21.2-5419. Happy to share files offline.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
_______________________________________________
phenixbb mailing list -- [email protected]mailto:[email protected]
To unsubscribe send an email to [email protected]mailto:[email protected]
Unsubscribe: phenixbb-leave@%(host_name)s
