[phenixbb] phenix.get_cc_mtz_pdb but allow for atom selections.

Pavel Afonine pafonine at lbl.gov
Sat Mar 3 18:59:04 PST 2012

Hi Nat,

to compute map CC one needs to define two maps. The source of maps can 
be PDB files, actual maps (for example, in Xplor or CCP4 or other 
format), Fourier map coefficients (that need to be FTed to get actual 
maps), or any combination of the above.

To compute maps (as opposed to reading them in from input file), the 
options for input information are: file(s) with map coefficients or 
model. In latter case you also need to know which scattering dictionary 
to use: x-ray or neutron or custom user-defined.

Also one needs to define which grid points to use: atom level, residue 
level or any user-defined (the latter is missing in 
phenix.real_space_correlation and can be trivially added).
phenix.real_space_correlation automatically decides whether to use atom 
or residue level, depending on resolution (obviously, there is no much 
sense to compute cc per atom at say 4A resolution, while at 1A 
resolution cc per atom is justified and more informative than cc 
computed in any larger scale).

Also one needs to handle special cases properly. One of many is (of 
course) hydrogen atoms, which you need to treat differently given the 
resolution and data type (x-ray or neutron).

Since we already have at least three phenix.*** tools to do more or less 
the same job (plus phenix.model_vs_data can output it too), adding 
another awesome one wouldn't probably be that awesome unless you somehow 
make clear what of the above it can and cannot do (or make it *really 
awesome* so it figures it all out automatically!).


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