I haven't been following the thread closely, so I'm not sure if this is relevant here, but I have experienced high anomalous difference map peaks from ANODE when a straightforward calculation didn't give strong peaks. The reason was SHELXC's sigma-based rejection, which significantly enhanced the peaks. Additionally, SHELXC and ANODE apply some B-factor blurring, which also contributes to peak enhancement to some extent.
Best regards, Keitaro On Thu, 6 Aug 2026 at 19:19, Phil Evans <[email protected]> wrote: > > Just for the avoidance of doubt, Aimless never removes the anomalous data, > even if “anomalous off” is set. that just affects the statistics > > Phil > > Sent from my iPad > > On 6 Aug 2026, at 10:44, Eleanor Dodson > <[email protected]> wrote: > > > CAUTION: This email originated from outside of the LMB: > [email protected]. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > [email protected] > > > -- > > I dont suppose the data is available to play with? There is obviously some > hitch somewhere that ought to be sorted.. > Eleanor > > On Thu, 6 Aug 2026 at 09:28, Andy Purkiss > <[email protected]> wrote: >> >> Dear Gottfried, >> >> Anode doesn't process the data itself; the processed data comes from the >> relevant pipeline used prior to Dimple/Anode running. What it does do is >> modify the phases from the native 'pdb' model, which in this case Dimple has >> molecular replaced into the data, with a phase shift from the anomalous data >> to generate the 'heavy atom' substructure. This is a different approach to >> the 'standard' anomalous map and, from the Anode paper >> (https://journals.iucr.org/j/issues/2011/06/00/fs5005/fs5005.pdf), can >> seemingly make use of weaker anomalous data to locate anomalous scatterer(s). >> >> Without splitting the data into smaller bins, it is hard to say where the >> anomalous signal goes to for this dataset. There are also considerations >> regarding the model (patches of negative difference density in the same >> region as the Anode peak) which will need solving before the peak can be >> confirmed and so more detailed analysis is needed to check that the peak >> isn't being influenced by errors in the phases from the model. However, as >> the model seems to have been changed by the presence of a ligand, an Anode >> peak from the Bromine would be expected. >> >> Anode does sometimes seem like "magic" especially with the size of the peak >> reported, but once the model is full built and refined, it generally seems >> that the peaks are 'real'. >> >> Hope this helps clarify. >> >> Andy >> >> ________________________________ >> From: Palm, Gottfried <[email protected]> >> Sent: 05 August 2026 16:06 >> To: Andy Purkiss <[email protected]>; [email protected] >> <[email protected]> >> Subject: Re: [ccp4bb] Question regarding Anomalous signal processing >> >> You don't often get email from [email protected]. Learn why this is >> important >> >> External Sender: Use caution. >> >> 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 <[email protected]> on behalf of Eleanor >> Dodson <[email protected]> >> Sent: 05 August 2026 12:21 >> To: [email protected] <[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 <[email protected]> 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 >> <[email protected]> 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 >> <[email protected]> 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). >> <Outlook-image.png.png> >> <Outlook-image.png.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! >> >> <Outlook-image.png.png> >> >> Regards, >> Jiazhi Tang >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> The Francis Crick Institute Limited is a registered charity in England and >> Wales no. 1140062 and a company registered in England and Wales no. >> 06885462, with its registered office at 1 Midland Road London NW1 1AT >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> The Francis Crick Institute Limited is a registered charity in England and >> Wales no. 1140062 and a company registered in England and Wales no. >> 06885462, with its registered office at 1 Midland Road London NW1 1AT >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
