We must remember that ramachandran ideals relate to amino acids in isolation and structural restraints - ie close contacts - can force interesting and correct deviations. Very precise high resolution structures can show omega angles of 160 ... Eleanor On Wed, 29 Jul 2026 at 09:30, Robbie Joosten < [email protected]> wrote:
> 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/ > ######################################################################## 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/
