You can evaluate your structure in MolProbity, then it would give a list of Ramachandran outliers similar to the output of COOT.
http://molprobity.biochem.duke.edu/index.php?MolProbSID=ktiuaj4c1v48mlgqq3inopfrf6&eventID=22 Regards, Burak ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Robbie Joosten <robbie_joos...@hotmail.com> Sent: 22 March 2018 10:52:57 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot Dear Laurant, Perhaps not a complete answer to your question, but more of a strategy. You can let the Ramachandran plot in COOT only show the outliers which would make everything a bit more tangible. Then only go for the massive outliers, these are the problems that need rebuilding (e.g. through peptide flipping). Many of the marginal outliers can be fixed through reciprocal space refinement with proper restraint weighting. Shameless plug: try PDB-REDO. It is (most of the time) quite good at tidying up your Ramachandran plot. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of > maveyrau > Sent: Thursday, March 22, 2018 11:27 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] coot: obtaining a clickable list of outiers in a > Ramachandran > plot > > Hi all, > > I’m currently refining quite a big oligomer (about 3500 residues) using > refmac/coot, at a 2.85 A resolution. The Ramachandran tool in Coot indicates > about 100 outliers, and I would like to check them individually… Is there a > way to get a clickable list of outliers? I know I can click on the > Ramachandran > plot directly, but with so many residues it’s quite impossible to go through > all of them… > > Thanks for any advices… > Laurent > ---------------------------------------------------------- > Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr > P I C T --- Plateforme Intégrée de Criblage de Toulouse > Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 > Département Biologie Structurale et Biophysique > http://cribligand.ipbs.fr http://www.ipbs.fr > 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE > Tél: +33 (0)561 175 435 Mob.: +33 (0)646 042 111 > ---------------------------------------------------------- > > >
