[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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