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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
