Dear all,
I'm also a bit confused ... there is no specialised "processing for
Anode" mode as far as I can see. Aftere all, Anode is computing
anomalous difference Fourier maps as one would do with e.g. plain FFT,
right? There is additional analysis of the map afterwards (peak
picking etc), but the actual map computation should be very standard
(look for "anomalous" in [1]), right?
It looks to me like some basic mixup with handling the data processing
and/or scaling stages - or picking the wrong MTZ file at the end
... maybe triggered by some ANO/noANO and/or FRIEDEL'S_LAW= TRUE|FALSE
confusion in the software?
Of course, it could also just be a case of a SG mixup (e.g. one comes
out as P2 when it should be P21 or such) or an alternative indexing
scheme picked ... so many banana skins to look out for ;-)
Cheers
Clemens
PS: processing the data with an explicit reference MTZ file helps
avoiding any hicups on that side
[1] https://www.ccp4.ac.uk/html/fft.html
On Wed, Aug 05, 2026 at 05:06:12PM +0200, Palm, Gottfried wrote:
> Dear Andy,
> could yould elaborate on this a bit: I understood, that processing
> for Anode results in higher resolution than processing with Aimless. I
> am curious why this would be the case, as this would affect other data
> sets as well. Or is it only the low resolution ( 7 Ang) of the cc
> anom? But then, how can Anode squeeze out a decent 8 sigma peak?
> Greetings
> Gottfried
> Am Mittwoch, den 05-08-2026 um 14:18 schrieb Andy Purkiss:
>
>
>
>
> Having looked at the data with Jiazhi, the issue is that the phased
> peak from Dimple/Anode is at 8 sigma and this shows the peak clearly
> in the anode map. However, the anomalous data from Aimless shows
> quite a low resolution (between 7 and 8 Ang) before the cc anom (and
> other anomalous stats) drops to the level of noise. There were
> multiple sweeps of data collected and the anomalous signal may also
> have been affected by the automated multiplex processing of the
> datasets together. The data appears quite low resolution (around 3.1
> Ang)
>
>
> There are also some issues with the model fitting the data in the area
> of the anode peak, possibly due to the ligand binding changing the
> local protein structure. There is also a percent or two increase in
> the cell dimensions compared with the search model.
>
>
> Andy
>
>
>
> -------------------------
>
> From: CCP4 bulletin board on behalf of Eleanor Dodson
> Sent: 05 August 2026 12:21
> To: [email protected]
> Subject: Re: [ccp4bb] Question regarding Anomalous signal processing
>
>
> External Sender: Use caution.
>
> But the anomalous difference is not lost - there is a clear peak of 8
> Sigma..
> E
>
>
> On Wed, 5 Aug 2026 at 11:42, Zhen L wrote:
>
>
>
> Hey Jiazhi,
>
>
> One thought that came to mind is whether the Friedel pairs were kept
> separate during processing in AIMLESS. If they were averaged at that
> stage, the anomalous differences would be lost, which could
> potentially explain why the ligand is visible in the 2Fo–Fc map but
> not in the anomalous map.
>
>
> All the best,
> Zhenyao Luo
>
>
>
>
>
> On Wed, 5 Aug 2026 at 20:29, Eleanor Dodson wrote:
>
>
>
> Hmmm - it is a good strong peak from the anom map. Hard to diagnose a
> problem without more information..
> There isnt some spacegroup issue is there - dimple selecting one
> indexing option and aimless another perhaps?
> Can you send your data processing log? That could help.
>
> Eleanor
>
>
> On Wed, 5 Aug 2026 at 10:49, Jiazhi Tang wrote:
>
>
>
>
> Dear all,
>
>
> I got a question regarding Bromine anomalous signal processing.
>
>
> I used a Br tagged chemical library for crystallographic drug
> screening. The crystals are shot at Diamond I03 with Br edge assigned.
> Diamond has a fantastic ISPYB feature which reveals the anomalous
> signal after auto processing by dimple. I can see some compound hits
> with reasonable anomalous signals (see below).
> image.pngimage.png
> However, when I downloaded the dials file (unmerged mtz) and process
> myself using ccp4 (aimless>identify contents>phaser>refmac), the
> anomalous signals are not visible in the anomalous map although the
> compound density is clear in 2Fo-Fc map. Does anyone know if I have
> missed anything during the data processing to reveal the anomalous
> signals properly? Much appreciated for any help!
>
>
> image.png
>
>
> Regards,
> Jiazhi Tang
>
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