Dear Renu,
Bernhard is probably on the right track. It is likely that your crystal
diffracted to substantially higher resolution than 1.7A, and that its
diffraction was sharply truncated by the edges of a detector placed too far.
If so, the sharp truncation in reciprocal space of the Fourier coefficients
going into your map calculation will cause "series termination" ripples in
your map in real space, that may well be the cause of what you see.
Remember that the average electron density in the unit cell is zero, so
that all the positive density visible as the chemically interpretable
features of the map is necessarily offset by negative density elsewhere,
although usually not sharply peaked.
Can you share one of your diffraction images? If not, you could process
your dataset with autoPROC [1]: the STARANISO pictures that are included in
the summary.html file would immediately show you whether it is the case that
a strong diffraction pattern was truncated by the detector edges.
With best wishes,
Gerard
[1] https://www.globalphasing.com/autoproc/
--
On Tue, Feb 22, 2022 at 11:56:50AM -0800, Bernhard Rupp wrote:
> Hmm…compliment, pretty darn good density map for 1.7 A….maybe look at the
> resolution cut-off.
>
> If it is at a significant level, it could be truncation ripples?
>
> Otherwise I second the noise opinion if it is already a well completed model.
>
>
>
> Cheers, BR
>
>
>
>
>
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of S
> Sent: Monday, February 21, 2022 21:34
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Negative density
>
>
>
> Hi All,
>
>
>
> I am getting this negative density in the centre of the ring. Could you
> please help me with this?
>
>
>
>
>
> Resolution: 1.7A
>
> 2FoFc - 1.5
>
> FoFc - 3.0
>
>
>
> Thanks in advance.
>
> Regards,
>
> Renu
>
>
>
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