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The placement in the centre of mass of a cluster of peaks would
explain the behaviour in many cases.
There are some cases though when Coot puts me "in the middle of
nowhere" as for occurrence of unexplained density peaks. ..
Not critical - just a bit hindering in the process of validation.

Jan


On Tue, Apr 27, 2010 at 5:26 PM, Paul Emsley <[log in to unmask]> wrote:
> Paul Emsley wrote:
>>
>> Jan Dohnalek wrote:
>>
>>>
>>> I have noticed that Coot puts me in irrelevant places when I use the
>>> Unmodeled blobs validation. It does its job but then the list of blobs sends
>>> me to perfectly interpreted places and I cannot see any uninterpreted
>>> blobs...
>>>
>>
>> I don't know why this should be, I have not seen it before.
>>
>
> Ingo K. reminds me that he and I corresponded about this issue some time
> ago.
>
> One problem could be that the symmetry and cell of the map does not match
> the symmetry and cell of the related protein.
>
> Or perhaps it's because Coot does not use the "viewing" contour level to
> generate blob map point clusters, i.e. it could be using a contour level
> much below what you are looking at.  Coot positions the view at the centre
> of a blob. If the blob consists of an "arc" of points (as is often the case)
> the centre of the blob will not be *in* the blob.
>
> Paul.
>



-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 390
Fax: +420 296 809 410