[phenixbb] Map quality

Pavel Afonine pafonine at lbl.gov
Fri May 15 09:37:03 PDT 2015

Hi Mohamed,

this is not a simple topic.. Two texts I suggest to have a look at are 
listed below I'm sure there are more). They may not give you a quick 
solution but perhaps will explain the issues.

Acta Cryst. (2014). D70, 2593-2606
Metrics for comparison of crystallographic maps

Acta Cryst. (2015). D71, 646-666.
FEM: feature-enhanced map

In a very nutshell,

- "1 sigma (or any other x sigma) level for one map may not be the same 
as 1 sigma (or any other x sigma) level for another map";
- Think of "global vs local". Somehow you need to quantify map quality 
- Map correlation (RSCC or map CC, for alternative names) may be a 
misleading metric is used without care: for example, two poor but 
similar map may give you high CC.

All the best,

On 5/15/15 9:10 AM, mohamed noor wrote:
> Dear all
> Is there a single (or a few) metrics that can be used to 
> quantitatively assess map quality instead of looking at each one in 
> Coot? For example, I want to compare the effect of having low 
> completeness in the low resolution shells.
> Thanks.

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