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In coot you have also the possibility to zoom into the ramachandran, this can helps maybe. Michel. > Le 22 mars 2018 à 18:57, Ashley Pike <[log in to unmask]> a écrit : > > Running phenix.molprobity yourpdbfile from command-line used to work – will give a molprobity_coot.py (from which when you calculate>run script in coot you will get a clickable list of rama/rotamer outliers and clashes) > > …………..although just checking it appears to not work with current COOT version distributed with CCP4 :( > > Does appear to work om my linux box if you launch coot via phenix (from command link type phenix.start_coot) > > HTH, > Ash > > From: CCP4 bulletin board <[log in to unmask]> On Behalf Of Kabasakal, Burak V > Sent: 22 March 2018 11:04 > To: [log in to unmask] > Subject: Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot > > 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 <[log in to unmask]> on behalf of Robbie Joosten <[log in to unmask]> > Sent: 22 March 2018 10:52:57 > To: [log in to unmask] > 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 <[log in to unmask]> On Behalf Of > > maveyrau > > Sent: Thursday, March 22, 2018 11:27 > > To: [log in to unmask] > > 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 > > ---------------------------------------------------------- > > > > > >