Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot

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 a écrit : > > Running phenix.molprobity yourpdbfile from command-line used to work – will > give a molprobity_coot.py (from

Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot

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

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=22 Regards, Burak From: CCP4 bulletin board

Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot

Hi Laurent, I seem to recall being able to click on outliers in the output of the phenix.refine GUI, which links to a Coot window. This would, however, require refinement in the Phenix suite rather than the CCP4 one. Best, Chris On Thu, Mar 22, 2018 at 10:27 AM, maveyrau

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.

[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