I'm still a bit confused about why there is a problem: why use SG numbers? "P 2 21 21" (or indeed "P22121") is clear and unambiguous. There is no need to use the numbers (and certainly not the weird CCP4 numbers like 3018 which I was trying to hide in Pointless
Phil On 2 Oct 2014, at 15:04, Kay Diederichs <kay.diederi...@uni-konstanz.de> wrote: > 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 >>> >>
