At present it uses actual map given at input, not map coefficients. Several people requested to add a functionality so that it can use map coefficients too, I will add this once I get a chance.

Pavel


On 5/19/15 5:27 AM, Smith Liu wrote:
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?
 
Smith






At 2015-05-19 13:25:28, "Pavel Afonine" <[email protected]> wrote:
Yes: phenix.map_comparison .

Pavel

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 <[email protected]>:
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,
Pavel


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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