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
<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
--
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
