Hi Catherine there are documented ways to model this kind of semi-ordered solvent, described here, for example:
https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 Pavel On Fri, Feb 6, 2026 at 3:50 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] > > > > ------------------------------ > > 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/
