Hi Marco, If you're working within the Phenix "ecosystem", you're probably aware that after each refinement run, a comprehensive validation report is generated and viewable in the Phenix GUI, it is interactively linked to Coot, allowing you to go over it and fix outstanding issues. Be sure to carefully and critically review it before PDB deposition.
You can also generate the PDB OneDep validation report (the long PDF file) directly from the Phenix GUI to see what the final submission will look like. Please note that different software tools—Phenix, Coot, PDB validation—may not always agree with one another. For example, one might flag something as an outlier while another does not. These discrepancies stem from differences in the geometric libraries or versions used by each tool. In borderline cases—such as residues near the edge of allowed/outlier regions on a Ramachandran plot—small numerical rounding differences can also lead to variation. We address these kinds of questions in training events like CCP4 Schools (like the one going on right now at Argonne) or Phenix workshops (such as the upcoming one at ACA), etc. I highly encourage people to attend if these types of questions still puzzle you! These training events happen periodically a few times a year around the globe. Good luck, Pavel On Sat, Jun 28, 2025 at 9:15 PM Marco Bravo < [email protected]> wrote: > Dear CCP4BB, > > I’m looking for guidance on the best practices for addressing geometry > validation issues such as plane outliers, bond angle outliers, and other > geometric deviations reported by the OneDep validation server during PDB > deposition. > > Specifically: > > What is the best workflow to correct or refine these outliers? > > Can these outliers be visualized directly in Coot? > > Are there recommended restraints or refinement strategies (e.g., in > REFMAC, Phenix) that help correct persistent geometry problems while > preserving model quality? > > Is there a way to highlight or auto-navigate to these specific outliers in > Coot, or to load the validation report in a way that helps locate them > efficiently? > > Any insight or tips from those with experience navigating OneDep feedback > would be greatly appreciated. > > Best regards, > Marco Bravo > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
