Hi Abhinav,

When does it write CC per atom vs per residue? Can you please elaborate?

it's resolution dependent.

Say you are looking at ARG (or something similar with long side chain), which has a few atoms sticking out of density, while the other atoms are well placed into density. Then if you compute CC for the whole residue it will still be high enough to mislead you thinking that everything is all right with this residue. However, if you compute CC per atom it will immediately red-flag these few atoms that are not in density.

Computing CC per atom actually makes only sense if density shows you atoms, that is the data resolution is high enough. For example, you would not want to compute CC per atom at resolutions like 3A or so.

Is there a way to tell the program to write CC one way or the other?

phenix.real_space_correlation allows more fine tuning. In particular it allows you to specify whether to output CC per atom or per residue.

Pavel