Any spurious blob on a symmetry axis is multiplied up of course.

And when you finish building side chains it may reduce in size.

But waters etc can sit on special positions - you just enter them with occ = 
0.5 and refine as usual..
Eleanor

On 5 Nov 2012, at 09:49, Crystal Xu wrote:

> Dear all,
> I am now determining a structure at 2.2 A resolution. The space group is C2, 
> and there is only one molecular in an ASU. During the refinement, some weird 
> electron density appears right on the two-fold axis. Does anyone have any 
> idea what could this be? Thanks a lot.
>    
> Best regards
>  
> Shutong Xu

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