The Drenth rule of thumb makes sense. Whether 2 in the macromolecular sense isomorphous structures are isomorphous, is a matter or resolution, and it has to do with the reciprocal space overlap function aka G-function. So up to a certain resolution, 2 data sets may be isomorphous, but at high resolution, not anymore.
In practical words, think of it in real space instead of FT reciprocal terms: to the myopic low-resolution eye, everything looks like a sphere and thus isomorphous. Just as in NCS, when you put on your high-resolution goggles, differences in real space (atom positions) become visible and the FT then becomes also non-isomorphous. In ML phasing, the non-isomorphism in essence pancakes your phasing probabilities due to increased variance. Result: The subtle art of data cut-off when exploiting isomorphism and shell-wise phase extension etc. 😊 Best, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Marius Schmidt Sent: Wednesday, December 20, 2023 14:36 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what is isomorphous? According to Jon, Isomorphous Replacement ALWAYS works, because it is only supposed to be isomorphous. Isomorphous difference maps can ALWAYS be calculated with sensible results, because the unit cells of the reference and the time-resolved data are only supposed to be isomorphous. Something is not right here... What is a "same unit cell?": unit cell params exact to the 6th digit, or maybe only to a fraction of the highest resolution, what fraction? Drenth says unit cells that differ by 0.25 x highest resolution can be considered isomorphous (0.5 A for 2 A data). What if 0.4 x highest resolution. Best Marius Marius Schmidt, Dr. rer. Nat. (habil.) Professor University of Wisconsin-Milwaukee Kenwood Interdisciplinary Research Complex Physics Department, Room 3087 3135 North Maryland Avenue Milwaukee, Wi 53211 phone (office): 1-414-229-4338 phone (lab): 414-229-3946 email: smar...@uwm.edu <mailto:smar...@uwm.edu> https://uwm.edu/physics/people/schmidt-marius/ https://sites.uwm.edu/smarius/ <https://www.bioxfel.org/> https://www.bioxfel.org/ Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 _____ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk <mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> > Sent: Wednesday, December 20, 2023 4:21 PM To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: Re: [ccp4bb] what is isomorphous? Unless you have a degree in maths, the IUCr's "Little Dictionary of Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on this matter (it's all to do with set / group theory, I think, and there are many more morphisms covered in about 6 pages: homo, epi, mono, endo, auto). Having discussed this with Ian Tickle, about 10 or 12 years ago, the formal (?) definition of isomorphous simply means that the unit cells of two or more crystals are the same, but the structure/molecule/compound/mineral, etc, does not even have to be the same. A sensible definition for dumb biologists might be to say that A and B are isomorphous, but C isn't. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com <mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail mobile -------- Original Message -------- On 20 Dec 2023, 20:15, Hekstra, Doeke Romke < doeke_heks...@harvard.edu <mailto:doeke_heks...@harvard.edu> > wrote: Dear colleagues, Something to muse over during the holidays: Let’s say we have three crystal forms of the same protein, for example crystallized with different ligands. Crystal forms A and B have the same crystal packing, except that one unit cell dimension differs by, for example, 3%. Crystal form C has a different crystal packing arrangement altogether. What is the right nomenclature to describe the relationship between these crystal forms? If A and B are sufficiently different that their phases are essentially uncorrelated, what do we call them? Near-isomorphous? Non-isomorphous? Do we need a different term to distinguish them from C or do we call all three datasets non-isomorphous? Thanks for helping us resolve our semantic tangle. Happy holidays! Doeke ===== Doeke Hekstra Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS), Director of Undergraduate Studies, Chemical and Physical Biology Center for Systems Biology, Harvard University 52 Oxford Street, NW311 Cambridge, MA 02138 Office: 617-496-4740 Admin: 617-495-5651 (Lin Song) _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &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/
