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
<[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
--
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
