Hi Ian,
I'm afraid that I will maintain my opinions that
- crystallography is elegant and unambiguous and should be kept like
that. The ITC even in the latest 2006 incarnation links space group
number 17 to "P 2 2 21" and 18 to "P21 21 2" (see e.g.
http://it.iucr.org/Ab/ch7o1v0001/sgtable7o1o018/ but unfortunately this
seems to require a license).
- throughout crystallography, symmetry is more important than cell
metric which means, in the case of space groups 17 and 18, that
enforcing of a convention/ convencience/ rule a<b<c will be misleading
in (statistically) 2 out of 3 cases, and I have evidence from outside of
my group that default application of this has lead to very real problems
in structure solution.
- extracting information from ("reading and trying to understand") a
logfile is _exactly_ what a logfile is meant for.
I do agree that in your use case it may be helpful to order a<b<c as
long as the symmetry is unknown. I also do understand that the H-M
symbols allow to describe the different settings, but this is a level of
complication that is not necessary to understand for todays's typical
crystallographer, because fortunately e.g. the C121 setting is
practically uniformly used (and chosen by POINTLESS, as far as I
understand) to represent C2 crystals. I just wish the same were true for
space groups 17 and 18. Importantly, this would prevent no-one from
using a different setting if s/he wishes, but the setting chosen by the
software should not depend on the mercy of the cell axes.
This is my last message in this meanwhile highly confusing thread.
best,
Kay
Am 03.10.14 um 17:13 schrieb Ian Tickle:
>
> Hi Kay
>
> On 2 October 2014 15:04, Kay Diederichs <[log in to unmask]
> <mailto:[log in to unmask]>> 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
