[phenixbb] Map quality

Smith Liu smith_liu123 at 163.com
Tue May 19 05:27:47 PDT 2015

Dear Pavel,
Can phenix.map_comparison be used to compare CCP4 map and mtz map? How to input map files in order to use this command?

At 2015-05-19 13:25:28, "Pavel Afonine" <pafonine at lbl.gov> wrote:
Yes: phenix.map_comparison .


On 5/16/15 12:28 PM, Murpholino Peligro wrote:

So...Is there a tool/program/formula to get equivalent sigma levels between maps so they can be compared?

2015-05-15 11:37 GMT-05:00 Pavel Afonine <pafonine at lbl.gov>:
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 locally.
- 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.


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