Hello,
I was just wondering whether there is some other tools in eg CCP4, Phenix or CNS to calculate real-space R in the general way in absolute values.
related to your question: in PHENIX you can get a table of map CC (computed between model and 2mFo-DFc maps), and the value of mFo-DFc and 2mFo-DFc maps at atomic centers (in sigmas), along with occupancies and B-factors. This can be reported per residue or per atom. The real-space R-factor is not computed - well, firstly, no-one asked for this feature (I can add it if really wanted), secondly, it feels to me that the triplet of values {map CC, 2mFo-DFc, mFo-DFc} is more than enough, and also I'm not sure I know how to interpret the real-space R-factor -:)
Tools to get this: - from PHENIX GUI: "Comprehensive validation" - from the command line: phenix.model_vs_data model.pdb data.mtz or phenix.real_space_correlation parameters.par Let me know if you have any questions about the above programs. Pavel.
