I think we’ve strayed a bit from Doeke’s original question involving crystals A, B and C, where I think the consensus opinion would be that we would refer to crystal C as not being isomorphous to either A or B.
On the question of what “isomorphous” means in the context of related crystals, I’m not sure we have complete consensus. I would tend to say that any two crystals are isomorphous if they have related unit cells and similar fractional coordinates of the atoms, so that (operationally) their diffraction patterns are correlated. However, there might be differences of opinion on whether two crystals can be considered isomorphous if one has exact crystallographic symmetry and the other has pseudosymmetry. (I would probably be on the more permissive side here.) In principle, I suppose being isomorphous (“same shape”) should be a binary decision, but in practice we’re interested in the implications of the degree to which perfect isomorphism is violated. So I would tend to use the term “poorly isomorphous” for a pair where the correlation between the diffraction patterns drops off well before the resolution limit. Crick was focused on percentage change in cell dimensions, but Bernhard is right that what matters is the ratio between the difference in cell lengths and the resolution of the data. It’s a bit counter-intuitive, but the effect of the difference between cell edges of 20 and 25 is the same as for cell edges of 200 and 205! By the way, the first time I learned this was from K. Cowtan and I hadn’t realised it’s also in Jan Drenth’s book. For isomorphous replacement (something some of us dimly remember from the days before AlphaFold), being poorly isomorphous is bad, but for cross-crystal averaging the more poorly isomorphous the better, because the molecular transform is being sampled in different places in reciprocal space. Best wishes, Randy Read > On 21 Dec 2023, at 10:53, Jon Cooper > <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hello Harry, > > I think this is the paper you mean: > https://scripts.iucr.org/cgi-bin/paper?S0365110X56002552 > > They gave depressingly low estimates of how much the cell dimensions could > change in order for isomorphous replacement to still work. In reality, unit > cells can shrink and swell, but the fractional atomic coordinates remain > relatively unchanged (right?) so bigger unit cell differences still allow the > method to work. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > Sent from Proton Mail mobile > > > > -------- Original Message -------- > On 21 Dec 2023, 09:07, Harry Powell < > 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Didn’t Francis Crick have something to say about this in the early 1950s? > I’m sure it was published but off the top of my mind I can’t think where (one > of the more “established” members of this community will be able to give > chapter and verse)! If you want to read something a little more detailed than > people have mentioned here, there’s a “Methods in Enzymology” chapter by > Charlie Carter (?) et al from the early part of this century on the subject - > again, I can’t remember exactly who or when. Have a good break (which reminds > me to register for the CCP4 Study Weekend)! Harry > On 21 Dec 2023, at 08:04, > Tim Gruene wrote: > > Hi Doeke, > > you can take the coordinates of B and do > a rigid body refinement > against the data from A. If this map is sufficient > to reproduce model A > (including model building and more refinement cycles), > then B is > isomorphous to A. You can do this the other way round, and the > result > may not be the same - hence, the mathematical definition of > isomorphous > is not identical to the practical use of 'isomorphous' > structures when > it comes to phasing. You can repeat this for each side of > the triangle > (each in two directions) in order to label the semantic > triangle. > > Merry Christmas, more peace on earth and sanity for the > elections in > 2024! > > Tim > > On Wed, 20 Dec 2023 20:15:17 +0000 "Hekstra, > Doeke Romke" > 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&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/ > > > > -- > -- > Tim Gruene > > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > > ######################################################################## > > > 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/ > ######################################################################## 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/ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## 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/
