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 <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
