| 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 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
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
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
External Sender:
Use caution.
But the anomalous difference is not lost - there is a clear peak of 8 Sigma..
E
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
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.
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!
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
|
