To give a short practical rather than a lengthy philosophical answer: - in real space: you can try Ramachandran restraints or secondary structure restraints -- indeed, both can be switched on in Coot in the refinement and regularisation parameters window (R/RC button in the top right corner). Or can try prosmart restraints as mentioned by others. And for the super-lazy: Extensions-->All Molecule-->Refine/Improve Ramachandran Plot.
- in reciprocal space: try restraints to a higher res reference structure that has better quality, e.g. prosmart for refmac or reference coordinates in buster. (But if you are indeed after a philosophical answer: with all due respect to those who believe in the sanctity of the Ramachandran plot as a validation tool, it seems that times are changing and many crystallographers now prefer better quality structures over pedantic validation tools… The Ramachandran plot is one tool in the validation toolbox and should be used as such, i.e. in the context of many other quality criteria, such as backbone geometry, rotamers, clashes, density fit etc, some of which are restrained or are refinement parameters anyway.) From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Michael Murphy Sent: 25 February 2015 17:09 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] adjusting bad Ramachandran angles Does anyone know of a way to adjust Ramachandran angles so that they fall within the preferred range? Either in Coot or possibly some online server? I have been trying to do it manually without much success, I was wondering whether there might another way to do it. -Thanks ________________________________ AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
