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 have to define the setting if you refer to the standard symbol. I'm aware 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! Cheers -- Ian On 2 October 2014 10:25, Kay Diederichs <[email protected]> wrote: > On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans <[email protected]> > 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 <[email protected]> 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 >
