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 <ashley.p...@sgc.ox.ac.uk> 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 <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Kabasakal, > Burak V > Sent: 22 March 2018 11:04 > To: CCP4BB@JISCMAIL.AC.UK > 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 <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 > > ---------------------------------------------------------- > > > > > >
