Hi Kai, There are several things to consider here: - In Coot you may be using Ramachandran restraints which make things look okay even when there is a modeling error. This is mostly an issue at low resolution. What helps a lot is to look at main chain hydrogen bonds and make sure you don't have any clashes. Try doing peptide flips if you are not sure about the current backbone conformation. - The magnitude of outliers is something to keep in mind. Ff something is just outside the main Ramachandran plot area, in many cases it is fine. You can have a look at the Ramachandran Z-score when you have fixed the obvious model errors and see how that develops after different cycles of refinement and interactive rebuilding. Tighter restraints in general typically improve your Ramachandran plot because they also give tighter Van der Waals restraints. Steric hindrance is the main cause of the Ramachandran distribution existing in the first place. - In Refmac and Phenix you can use a reference structure to keep your refinement stable. The implementations are very different, but they can help stabilise your refinement. PDB-REDO has homology-based hydrogen bond restraints that do a similar thing, again with a completely different implementation. - In Refmac you have gelly-body restraint to stabilise your refinement. This too can help your model from drifting off too quickly from the state you had in Coot. They work very well (PDB-REDO uses them too). - Phenix also has Ramachandran plot restraints. Personally, I'm not a big fan of that because it improves cosmetics, but your Ramachandran plot distribution comes from other interactions that are already restrained. That said, at very low resolution they might nevertheless be helpful. If you use them, that effectively invalidates the Ramachandran plot validation (although Rama-Z is reasonably robust to that), so you should explicitly mention that you have used them in the method section of your paper.
Note that all the restraints in Refmac and Phenix work best if your model is correct, so please first make absolutely sure that the drift in refinement doesn't come from model errors. HTH, Robbie > -----Original Message----- > From: CCP4 bulletin board <[email protected]> On Behalf Of > [email protected] > Sent: Wednesday, July 29, 2026 03:49 > To: [email protected] > Subject: [ccp4bb] About the difference of Ramachandran conformations > between Coot and phenix/Refmac5 > > Dear all > > In Coot, I have successfully adjusted the Ramachandran conformations of the > amino acids to reasonable values. However, after refinement, I notice that > many > amino acids deviate again from the allowed Ramachandran regions.Could you > kindly suggest any methods or strategies to prevent or mitigate this issue? > > Sincerely > > Kai > > > ________________________________ > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
