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 <[log in to unmask]> wrote:
> On Thu, 2 Oct 2014 11:58:42 +0100, Ian Tickle <[log in to unmask]> 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 <[log in to unmask]>
>> 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
>>>
>>
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