With the successful introduction of racemic crystallization to
macromolecular, a large number of possible space groups have been opened
up to this audience. You can find examples in the PDB of space groups P
-1 (i.e. "P 1-bar"), I -4 2 d, etc.
On 10/02/14 06:51, George Sheldrick wrote:
> 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
>>
>
>
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
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