Hi Catherine
Just a couple of ideas from my side: - draw all the molecules (by symmetry) with a fairly large radius, to see the whole packing (you likely did, but in the pictures you shared, there’s only the ASU content). Maybe there’s little more to model actually - your first picture does suggest some more can be modeled in: I would say always play around with the Fourier maps’ contours (both for the 2Fo-Fc/blue, as well for the diff Fo-Fc/green), especially lowering them. Noise will show up higher everywhere, but you might be able to discern more continuity in the spots you’re focusing on. Sometimes blurring (blurring/sharpening functions in coot) the map is also helpful for this, for a first interpreting task will reduce details, yet enhance low-resolution/envelope features. (nice to learn about modelcraft from ccp4, thanks Dave!) my 2 cents Ale > On 6 Feb 2026, at 9:46 AM, David Briggs > <[email protected]> wrote: > > 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] > <mailto:[email protected]>> on behalf of Catherine Back > <[email protected] > <mailto:[email protected]>> > Sent: Friday, February 6, 2026 11:48:48 AM > To: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[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] <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 > 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 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/
