On Thu, 2 Oct 2014 11:58:42 +0100, Ian Tickle <ianj...@gmail.com> wrote:
>Hi, we shouldn't be using numbers at all (CCP4-style or otherwise, since >no-one else outside the MX community uses these). We should be using the >unique full Hermann-Mauguin symbol, since the 'standard setting' space >group number in IT obviously does not uniquely define the setting, and it's >the setting that matters. Note that the standard setting symbol P2221 >means 'either P2122 or P2212 or P2221' according to the a<=b<=c convention >(this is universal amongst the crystallography communities), so you still Once again, citing from ITC Vol A Table 9.3.2 (p. 747 in my 1995 edition) , these "conventions refer to the cell obtained by the transformations from Table 9.3.1. They have been chosen for convenience in this table". To me, this indicates that a<b<c _could_ be obtained _if_ one were to transform. But the question is: why would one want to transform? I don't see "sticking to the original indexing" as a convincing convenience. >have to define the setting if you refer to the standard symbol. I'm aware My copy of ITC Vol A says (p 41) about Table 3.2: "the 'standard' space group symbols ... are printed in bold face". The Table has "P 21 21 2" (18) and "P 2 2 21" (17) in bold face. There is no ambiguity here. >that some software uses the list of general equivalent positions to define >the space group but IMO that's overkill. If I wan't to talk about space >group F432 you can't expect me to recite the list of 96 g.e.p.s! - the H-M >symbol is sufficient. There are of course other cases besides P2221 where >the setting is ambiguous (e.g. C2/A2/I2 and various cases of origin >shifting), so using the correct symbol for the setting is critical. > >The most important features of any convention are a) that it's documented >in an 'official' publication (i.e. not informal such as software >documentation, otherwise how am I supposed to reference it?), and b) >everyone subscribes to it. If you think we should be using a different >convention then I want to see the proper documentation for it, with >everything spelled out in excruciating detail (so it should be at least as >thick as ITC!). It seems to me that ITC fulfils these requirements >admirably! Switching the default in POINTLESS from "SETTING CELL-BASED" to "SETTING SYMMETRY-BASED" would make me happy, but more importantly, would avoid a lot of problems. thanks, Kay > >Cheers > >-- Ian > >On 2 October 2014 10:25, Kay Diederichs <kay.diederi...@uni-konstanz.de> >wrote: > >> On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans <p...@mrc-lmb.cam.ac.uk> >> wrote: >> >> >Be careful: the International Tables space group number may be ambiguous. >> For example sg number 18 may refer to P 21 21 2 or its permuted settings P >> 21 2 21 or P 2 21 21, if you follow the "proper" IUCr convention that >> primitive orthorhombic space groups have a<b<c >> >> I would like to point out that there is an alternative interpretation of >> the International Tables (Vol A, 4th ed. 1995). In that interpretation >> (which e.g. XDS follows) space group 18 has the 'standard' space group >> symbol, "P21 21 2" (bold letters in Table 3.2). This is of course not >> ambiguous at all; the pure 2-fold then corresponds to the "c" axis and >> there is always a permuation of axes to achieve this. As a result, the axes >> are not necessarily ordered such that a<b<c . The latter ordering is just a >> "convention" which was "chosen for convenience" and the "convention >> refer(s) to the cell obtained by the transformations from Table 9.3.1" >> (citing from table 9.3.2) - in other words, the convention is fulfilled >> _after_ the transformation (which of course is just order-permuting while >> keeping right-handedness) - nothing new here. >> >> In my understanding, CCP4 developers have (years ago) understood this >> "convention" as a "condition", which lead them to invent "CCP4 space group >> symbols" 1017 and 2017 as well as 1018, 2018, 3018. This also seems to be >> the reason for the default being "SETTING CELL-BASED" in POINTLESS. >> >> Users of XDS should be aware that by default, POINTLESS therefore permutes >> the axes such that a<b<c . This however may lead to space groups 1017 / >> 2017 / 1018/ 2018/ 3018 - indicated in the MTZ file, but not in the >> POINTLESS log file (last I checked). >> >> In consequence, XDS will use the space group 17 or 18 (which is what >> POINTLESS reports), but the user must provide the correct ordering (which >> does not necessarily mean a<b<c) of cell parameters in XDS.INP. The easiest >> way, for XDS users, would be to run POINTLESS with the "SETTING >> SYMMETRY-BASED" option (I wish the latter were the default because the >> default SETTING CELL-BASED has no advantages that I can see). Or they use >> the "good old manual way" of inspecting, by eye, the systematic absences >> along H00 0K0 00L - this cannot fail. >> >> To me, "symmetry trumps cell metric" so "SETTING SYMMETRY-BASED" should be >> the default. >> >> I'm harping on this because I have recently seen how a Molecular >> Replacement solution was not obtained in space group 18 because of the >> misleading (I'd say) ordering a<b<c . >> >> I'm probably also harping on this because it took me so many years to >> discover this failure mode, and I would like to prevent others from falling >> into this trap. >> >> HTH, >> >> Kay >> >> >> >> > >> >The space group names are unambiguous (though also watch out for R3 & R32 >> which are normally indexed as centred hexagonal, but could be indexed in a >> primitive cell) >> > >> >Phil >> > >> > >> >On 30 Sep 2014, at 13:07, Simon Kolstoe <simon.kols...@port.ac.uk> wrote: >> > >> >> Dear ccp4bb, >> >> >> >> Could someone either provide, or point me to, a list of space-groups >> relevant to protein crystallography just by space group number? I can find >> lots of tables that list them by crystal system, lattice etc. but no simple >> list of numbers. >> >> >> >> Thanks, >> >> >> >> Simon >> >
