The strange thing is that small molecule crystallographers do not suffer
from this problem, because they don't use space group numbers! This is
just as well, because instead of just 8 combinations of primitive
orthorhombic space groups and settings, they have to consider 111 (if I
have counted correctly).
George
On 10/02/2014 11:50 AM, Frank von Delft wrote:
> I second that! The default should be symmetry based... cells stretch
> and shrink, but symmetry is harder to change. (i.e. from crystal to
> crystal.)
>
> (I thought all CCP4 programs have supported this for ages.)
>
>
>
> On 02/10/2014 10:25, Kay Diederichs wrote:
>> On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans
>> <[log in to unmask]> 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 <[log in to unmask]>
>>> 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
>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
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