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.
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