Dear Ian, Kay et al.,
The omnipotent CheckCIF program that is used to check all small molecule
structures submitted to /Acta Cryst./ and many other journals requires
(a) the H-M space group name, (b) the Hall symbol and (c) the list of
equivalent positions, and checks that *all three* are consistent!! Ralf
Grosse-Kunstleve implemented the Hall symbols in cctbx so I presume that
all Phenix programs understand them.
Each Hall symbol corresponds to a list of general equivalent positions.
However Hall symbols are not a perfect solution because (a) it is
possible to have more than one Hall symbol for the same set of
equivalent positions and (b) although the lists of possible Hall symbols
are rather extensive, they do not cover all possible combinations of
space groups and settings. For example the IUCr and Ralf's lists include
the common non-standard setting P21/n (Hall: -P 2yn) for space group
P21/c (Hall: -P 2ybc) but not the more rarely used non-standard setting
B21/d of the same space group. In terms of equivalent positions this
setting causes no problems, the SHELX notation for it is:
LATT 6
SYMM 3/4+X, 1/2-Y, 1/4+Z
So I have obstinately insisted for the last 40 years that the list of
equivalent positions is the best way of specifying symmetry. It would
have saved a great deal of confusion.
I also do not accept the argument that a list of equivalent positions is
error prone. Firstly they are almost always put there by a program, not
a human being, and secondly SHELXL and other programs check them for
internal consistency.
Best wishes, George
On 10/03/2014 07:58 PM, Ian Tickle wrote:
(a) The IUCr has, in its wisdom, decided to use the */Hall space
group symbols/* to settle the matter. See International Tables for
Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2//and
/Acta Cryst./ (1981). A*37*, 517-525. These are obligatory input
for CheckCIF as part of small molecule verification. 'P 21 21 21'
becomes 'P 2ac 2ab' and 'P 21 2 21' becomes equally logically 'P
2ac 2ac'. Fortunately for the users, SHELXL-2014 derives the Hall
symbols from the symmetry operators.
I agree that would make a lot more sense but it's taken many years to
get to where we are now so I can't see this happening any time soon!
(b) Isn't it time to introduce the 'R 3' or 'H 3' or 'R 3 :H'
issue again?
Yes by all means: the H cell in ITC (triple cell) means something
completely different from the PDB idea of H cell, so it's the PDB we
have to tackle. But again, realistically is it going to happen?
(c) As pointed out already, small molecule crystallographers never
have this problem because the coordinates of the general position
are used to define the space group symmetry unambiguously, in
conventional settings or otherwise. Ian's argument that there
could be too much to type in for cubic space groups is irrelevant,
because the list is always generated by a program (e.g. XPREP or
its clones).
I assume that the Hall symbol unambiguously defines the list of
g.e.p.s (if it doesn't then what use is it?). Assuming that it does
then why not use it in place of the list and look up the g.e.p.s from
a file (e.g. syminfo.lib)? As I said before, comparing lists of
g.e.p.s seems to be overkill and prone to errors (and in fact I think
there have been bugs in the CCP4 implementation). Simple comparison
of the Hall symbols would appear to be a lot less error-prone!
Cheers
-- Ian
George
On 10/03/2014 05:13 PM, Ian Tickle wrote:
Hi Kay
On 2 October 2014 15:04, Kay Diederichs
<[email protected]
<mailto:[email protected]>> wrote:
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.
I'm sorry, unfortunately my edition of ITC-A (5th Ed., 2002) is
later than yours (4th Ed.) and I have been unable to get hold of
a copy of the edition that you refer to. In my edition the table
equivalent to your 9.3.2 seems to be 9.3.4.1 on p.758 and there
doesn't seem to be a table equivalent to your 9.3.1 (the only
other table in that section is 9.3.5.1 but that doesn't seem to
be relevant). Also I am unable to match up the text that you
quote with what I see in my edition: it seems to be completely
different. So it's very difficult to comment. According to the
Foreword "The present 5th Edition is much more extensively
revised than any of its predecessors ..." so I can only assume
that the text that you quote was considered unclear and was
removed. But I agree that if one is concerned with a specific
structure without reference to any other structure, why would one
want to transform anything? It makes no sense. The conventional
setting is selected according to table 9.3.4.1, end of story.
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.
Again I'm sorry but I don't see that text in my edition (p.41 is
just a list of references for Chap. 2) and I can't find the
corresponding section in my Edition. However I do agree that the
standard symbol for each space group is printed in bold face in
the top-left corner of each double-spread page dealing with that
space group (also in smaller type in the top-right corner).
Perfectly true observation I agree but how is it relevant? The
230 standard symbols are the names of the 230 equivalence classes
defined on the complete set of possible alternate settings for
the equivalence relations consisting of the possible rotations
and/or translations relating those alternate settings. Since
they only serve as labels one could equally well have chosen the
ordinals 1 through 230 (which are actually given equal prominence
to the names).
The important point is that the standard symbol is only the
_name_ of the equivalence class and that this is not sufficient
for dealing with crystal structures and calculating structure
factors etc.: one must specify which element of that class, i.e.
from the subset of possible unique _settings_ that are members of
that class, to use. For example in the 5th Ed. the 10 possible
settings for standard symbol C2 are shown, with the full H-M
symbols C121, A121, I121, A112, B112 etc. So e.g. A121 is one of
the allowed conventional settings in the equivalence class C2.
Notice that the standard symbol C2 is _not_ a full H-M symbol: it
doesn't need to be, since it's only a name and it doesn't need to
carry any information. Its only requirement is that it's unique
among the 230 equivalence classes. Similarly the page for
standard symbol P2221 shows the possible settings (at least in my
Ed.) P2221, P2212 and P2122. In this case the standard symbol
happens to be the same as one of the full H-M symbols of the
alternate settings but that's not a requirement, any unique name
would have done equally well. Also in the setting P2221 there
obviously remains an ambiguity concerning the assignment of the a
and b axes. How is that resolved? You will probably say a<b but
ITC doesn't specify that as a condition anywhere, it just says
"a<b<c", not "a<b<c unless it's P2221 or P21212 when it's a<b"
(the first condition doesn't require exceptions).
Have you considered the fact that not all possible alternate
settings are listed for all space groups? For example no
trigonal, tetragonal or hexagonal settings have a or b unique
(you can find many other examples in the monoclinic &
orthorhombic systems, e.g. there are no B settings in
orthorhombic). Why is that? What's so special about the
settings that are listed that doesn't apply to all the ones not
listed? You can be sure it's by very careful design since
printing space was at a premium when the tables were first
published (I spent my first post doc. at the Laboratorium voor
Struktuurchemie at the Rijksuniversiteit Groningen at the same
time Dirk Fokkema was there: he wrote the software for the
computer-driven typesetting of the main Vol. A table of space
groups for his Ph.D. thesis; we had a number of discussions about
space groups and I can assure you that the table was very
carefully designed!). The answer is that the settings listed are
strictly those that satisfy the requirements of the rules on
conventional cells in table 9.3.4.1, no more, no less. The
appropriate setting is selected from the members of the
equivalence class of the space group in question according to
those rules.
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.
Maybe the answer is to fix the problem with pointless that you
highlighted originally, i.e. it's apparently reporting the wrong
space group in the log file! Actually extracting stuff from log
files is a very bad idea: log files are not guaranteed to remain
the same across different versions of the program! I learnt that
the hard way! Doesn't pointless output an XML file, or you could
just read the MTZ file header. That's what I do, it's much safer.
Cheers
-- Ian
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel.+49-551-39-33021 <tel:%2B49-551-39-33021> or -33068
Fax.+49-551-39-22582 <tel:%2B49-551-39-22582>
--
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
