[phenixbb] Filtering ordered solvent molecules based on secondary map

Pavel Afonine pafonine at lbl.gov
Tue Jan 4 18:05:22 PST 2011

>                 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,

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