For my own education, what would be the best way of calculating the correlation coefficient values for all the waters or ligands in a given model? What I want to do is get a sense for the relationship between electron density and correlation coefficient values for waters in my structure to understand how “strict” the default poor_cc_threshold value is and whether/how much I might want to raise it.

Continuing while waiting for boarding... Actually, looking at map CC alone is not too informative although is definitely good. Imagine you compare two densities both having max sigma value say ridiculously small like 0.1 sigma. In this case you will still get high map CC (by high I almost arbitrarily mean something like 0.7-0.8 and up to 1). I looked into this at some point and it seems like you need to look at both - map CC and actual density values. Of course this is very resolution dependent... Also, what matters is the region where you compute map CC. Say you have a large residue where only a couple of ending atoms are misplaced (not in density). In this case the map CC computed for the whole residue will still be good, so you will never catch those couple of atoms. Therefore, it's better to compute map CC per atom, and not per residue. But there is a trick here too. It makes sense to compute map CC per atom only when the map shows atomicity, so you can more or less determine individual atoms. At resolutions like 3A and lower you see a blob of density for a residue, and computing CC per atoms doesn't really makes sense... I'm not aware of any systematic research on this subject. I guess it can be a nice a month or two long project for a student.

Good luck,
Pavel.