All the (library) code is open source with a BSD license, so yes this is possible.
Cheers, Robbie > -----Original Message----- > From: Boaz Shaanan <bshaa...@bgu.ac.il> > Sent: Monday, January 18, 2021 22:57 > To: Robbie Joosten <robbie_joos...@hotmail.com> > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO > > Hi, > Will it be possible to include the rama-z analysis in Coot (perhaps as a > plugin)? > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jan 18, 2021 22:47, Robbie Joosten <robbie_joos...@hotmail.com> > wrote: > > Dear all, > > During the last CCP4 meeting, Oleg presented our collaboration with the > Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, > some asked for a convenient way to get this score. You are now welcome to > use: https://pdb-redo.eu/tortoize > > This is a quick and easy way to check you model. Just upload your structure > model (and restraints if you have non-standard compounds) and press > "calculate". You get the Ramachandran Z-score with an error margin and you > get the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in > WHAT_CHECK) for free. > > There are two more ways to get the score, that might be relevant for > specialized use: > 1) use the webservice to get the same values and the per-residue values in > an easy-to-parse JSON file. For example through curl with the command: curl > -F data=@1cbs_final.pdb -F dict=@/zata/ccp4- > 7.1/lib/data/monomers/a/ALA.cif https://pdb-redo.eu/tortoize. Note that > the "dict" value is optional. Any other POST on https://pdb-redo.eu/tortoize > would also work. > > 2) to analyse a very large group of models you are encouraged to install > tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with > a BSD license. > > The scores are also of course available after each PDB-REDO run: the Rama-Z > is one of the model quality metrics. All methods take PDB and mmCIF > formatted files as longs as they are valid, i.e. fit the current format > specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, > constructive feedback is appreciated. > > If you use Rama-Z, please do cite: > Sobolev et al. A Global Ramachandran Score Identifies Protein Structures > with Unlikely Stereochemistry; Structure; > https://doi.org/10.1016/j.str.2020.08.005 > > All the best on behalf of Team REDO, > Robbie > > ############################################################### > ######### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > <https://www.jiscmail.ac.uk/policyandsecurity/> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
