Just to add to Graeme and Dave's comments. I have seen similar 'extra' density when the spacegroup was lower symmetry than autoprocessing in P222 implied. Here P21 was the correct answer, but it wasn't the best of the three possible options due to tNCS confusing the indexing. Finding the correct answer needed molecular replacement in all three possibilities.
I would certainly try reprocessing in P1 and it is then possible to generate the full unit cell contents from the original solution with either Coot (or Zanuda) to save having to re-solve the structure. Hope this helps Andy ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Graeme Winter <[email protected]> Sent: 06 February 2026 13:27 To: [email protected] <[email protected]> Subject: Re: [ccp4bb] Crystal pathology diagnosis please External Sender: Use caution. In a case like this I would not trust the auto processing without question (says the original author of said auto processing) At the very least - - check over the indexing results - has it caught all the spots or > 90% of them - look at the indexed and unindexed spots in the reciprocal lattice viewer - if the latter are unrelated to the former (e.g. secondary crystal, ice, …) then it’s fine - but could be weak spots between strong ones indicating a larger cell with near-symmetry - look at the images with the integration results overlaid - are all the spots measured? Check at various points in the data set If all the spots are integrated, then xtriage etc. as others have suggested, and taking your model and trying refinement in P1 (e.g. pull integrated data down, scale in P1 or just use zanuda - also another’s suggestion) - also: check that the symmetry determination (logs should be there) show the P2?2?2? option as being just as good as the 3 x P2? options - if one P2 option is much better could be that the true symmetry is different Essentially looking over all the processing “decisions” with a critical eye will help you a lot here, happy to help (off list) if you would like more pointers All the best Graeme On Feb 6, 2026, at 5:48 AM, Catherine Back <[email protected]> wrote: Morning All, My colleague and I are trying to solve the structure of a long, alpha helical bundle protein. We thought it had solved well with 2 molecules in the AU (which had decent stats), but upon a closer look there are very large 'solvent channels' in the lattice, with green/blue density within. It looks like there are protein molecules, positioned lengthways to the molecules in the AU, within these channels which the autoprocessing (at Diamond Light Source) is not picking up. See images attached. I now have the image files and have been reprocessing them using xia2-DIALS in ccp4i2. I am unsure what kind of crystal pathology we're dealing with here. There is no twinning warnings or anything else really that the processing has identified. The space group is always identified as P212121, unit cell 34.8, 184.8, 202.3, 90.0, 90.0, 90.0. I've tried quite a few different things to get the software to fit molecules into the density, including manually extending the unit cell, but all the outputs have been wrong or had really bad stats. I'm wondering if the indexing is wrong, but I'm not sure how to sort this. There is clearly something going on here, which is either really obvious (that I'm not identifying because I'm an idiot) or it's something more complex. Any ideas/help will be much appreciated. Best wishes, Catherine Back Dr Catherine R. Back (she/her) Senior Post-doctoral Research Associate School of Biochemistry University of Bristol UK [email protected]<mailto:[email protected]> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <Screenshot 2026-01-22 at 10.39.07.png><Screenshot 2026-01-27 at 15.10.55 (2).png><Screenshot 2026-01-27 at 15.12.12 (2).png><Screenshot 2026-01-27 at 15.13.57 (2).png> ________________________________ 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 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/
