[phenixbb] Map quality
Pavel Afonine
pafonine at lbl.gov
Tue May 19 09:38:09 PDT 2015
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" <pafonine at lbl.gov> 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 <pafonine at lbl.gov
>> <mailto: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,
>> 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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>
>
>
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