I think this is only a problem in the primitive orthorhombic system
(at least I assume people don't want hexagonal axes along a, A & B
centred lattices etc, although there is no reason in principle why not).
Following some earlier discussions with Ian, Pointless now honours
(and preserves) a reference file (HKLREF) in eg P 2 21 21, and also
explicit reindex operations, but an initial indexing will still
enforce the "standard" setting eg P 21 21 2, because I accept the
"reference" setting from the cctbx library
ie suppose you have a crystal which when indexed with a <= b <= c and
Pointless decides unambiguously for the sake of argument) that the
axis along a is a 2-fold and the other two are 2(1) screws, ie space
group P 2 21 21.
At present this will be reindexed to the "standard" setting P 21 21
2, but is that what you want, or should it be left as a<b<c? Which
criterion takes precedence?
Phil
On 19 Sep 2007, at 17:54, Ian Tickle wrote:
Hi Sue
It's certainly true that the convention in the 1935 and 1952
editions of
IT Volume 1 *appeared* to be the 'standard setting' convention that
you
describe because only the 'standard' settings were listed, and this
was
the way that many crystallographers interpreted it (actually only
macromolecular crystallographers, the small molecule people stick
to the
IUCr convention), so this is probably where you're coming from.
However
the 1983 edition of Volume A clarified the situation and made it clear
that this was never the intention, so all the conventional settings
are
now shown on the SG diagram pages. P22121 & P21221 certainly are
defined in IT Vol. A - look on the diagram page for SG no. 18 & you'll
see them.
The 'standard symbol' for a space group is merely the heading on the
page used only for indexing purposes, so space groups P22121,
P21221 and
P21212 all have the same standard symbol P21212; hence the standard
symbol is not unique and can't be used to unambiguously define the
space
group. The 'standard setting' is merely the space group setting that
has the same name as the standard symbol. Even if that weren't
true do
we really want to be still sticking to a convention that was abandoned
25 years ago and doesn't a later convention override an earlier one
anyway?
Actually the convention in use is not the issue anyway, I don't care
which convention is used as long as all programs use the same
convention! - then I'll never need to permute axes (just as
fundamentally I don't care which co-ordinate format is used as long as
all programs use the same one, then I'll never need to reformat). So
Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive
orthorhombic), and therefore any program which doesn't support that
convention for any space group forces you to permute the axes
completely
unnecessarily.
-- Ian
-----Original Message-----
From: Sue Roberts [mailto:[EMAIL PROTECTED]
Sent: 19 September 2007 16:38
To: Ian Tickle
Subject: Re: [ccp4bb] arp/warp in p22121
Hi Ian
But there's an older convention, which is to use the space groups
settings defined in the International Tables - and P22121 is not a
standard setting.
Sue
On Sep 19, 2007, at 8:18 AM, Ian Tickle wrote:
I'm confused now, sticking to the IUCr convention should not
require any
axis permutation. My beef is specifically against unnecessary axis
permutations! Surely it's when the program doesn't support the
convention that you are forced to permute the axes?
Besides I did solve a structure in P22121 with Phaser so
I'm even more
confused!
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Airlie McCoy
Sent: 19 September 2007 15:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] arp/warp in p22121
The problem is specifically that ARP/wARP *doesn't*
support the IUCr
convention as given in IT (Vol. A, >= 1983 edition, Table
9.3.4.1, p.758
in 5th ed.) regarding choice of cell in primitive
orthorhombic space
groups, and I suspect in centred monoclinic ones also.
AFAIK ARP/wARP
and pointless are the only two CCP4 programs that currently
don't fully
support the IUCr convention
Phaser doesn't "support" the IUCr convention, and if it was
used for the
original MR in this case (I don't know whether it was or
not), then it
would have caused the "problem". We have had user requests to
change the
output to the IUCr convention, but other people get confused
if the axes
are permuted. So the choice will be made an output option -
Frank von Delft
suggested the keyword "IUCR [ON/OFF]"! Vote for your choice
of default
now...
Airlie McCoy
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Sue Roberts
Biochemistry & Biophysics
University of Arizona
[EMAIL PROTECTED]
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Therapeutics Ltd accepts no liability for damage caused by any
virus transmitted by this email. E-mail is susceptible to data
corruption, interception, unauthorized amendment, and tampering,
Astex Therapeutics Ltd only send and receive e-mails on the basis
that the Company is not liable for any such alteration or any
consequences thereof.
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