Hi Catherine, Have you shown the data to xtriage? (run by some pipelines at Diamond, or available as a standalone program in Phenix). The output might give you some hints.
You don't say what your current r free is at the moment, but if your phases are decent enough, I'd set modelcraft off on the data and go and get some lunch. That software is imo akin to witchcraft and has saved me a lot of manual tinkering to deliver a mostly complete asymmetric unit. It's found extra copies I didn't know I had, and even revealed proteolytic fragments that had been crystallised (I don't know how modelcraft behaved with coiled coils, bit probably still worth a punt). I'd also run Zanuda to check the space group (I always do this now, having been tricked by crystals in the past). Best of luck! Dave -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist, and Co-chair, Crick Staff Consultative forum Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours Mon-Fri 0900-1700 == about.me/david_briggs<https://about.me/david_briggs> | OrcID<https://orcid.org/0000-0002-9793-7339> | Google Scholar<https://scholar.google.co.uk/citations?user=DRKG5wAAAAJ> == "Would it not be better if one could really 'see' whether molecules...were just as experiments suggested?" – Dorothy Hodgkin ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Catherine Back <[email protected]> Sent: Friday, February 6, 2026 11:48:48 AM To: [email protected] <[email protected]> Subject: [ccp4bb] Crystal pathology diagnosis please External Sender: Use caution. 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] ________________________________ 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/
