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/
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
On Saturday, 04 October 2014 10:26:51 AM Kay Diederichs wrote:
I do agree that in your use case it may be helpful to order abc 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
If you know the indexing that you want, from a user's point of view it is much
easier to specify e.g. I want to choose spacegroup P6522 (with or without
spaces), rather than Oh what's the number, I'll have to go and look it up.
Phil
On 2 Oct 2014, at 21:12, Kay Diederichs
Hi Kay
On 2 October 2014 15:04, Kay Diederichs kay.diederi...@uni-konstanz.de
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
Since this discussion doesn't want to end. I should point out
(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*,
(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
By default I believe for most crystallographic applications, the hierarchy
is:the symmetry operators, but if absent the SG name (and this can be P21
21 2 or P 21 2 21 or whatever) , but that is absent and you are lazy you
can give the SG number.. And that can deal to confusion and should be used
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
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,
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
How does XDS decide on eg P 21 21 2 when say c b a? The initial indexing
may decide that the cell fits a primitive orthorhombic system, but I presume
that it will then have some convention, probably a b c, since the
identification of screws can only be done after integration, and even then
Hi, we shouldn't be using numbers at all (CCP4-style or otherwise, since
no-one else outside the MX community uses these). We should be using the
unique full Hermann-Mauguin symbol, since the 'standard setting' space
group number in IT obviously does not uniquely define the setting, and it's
the
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
Yes, we ran into exactly that issue as well.
Jūrgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Streetx-apple-data-detectors://4, W8708
On Thu, 2 Oct 2014 11:38:08 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
How does XDS decide on eg P 21 21 2 when say c b a? The initial indexing
may decide that the cell fits a primitive orthorhombic system, but I presume
that it will then have some convention, probably a b c, since the
On Thu, 2 Oct 2014 11:58:42 +0100, Ian Tickle ianj...@gmail.com wrote:
Hi, we shouldn't be using numbers at all (CCP4-style or otherwise, since
no-one else outside the MX community uses these). We should be using the
unique full Hermann-Mauguin symbol, since the 'standard setting' space
group
I'm still a bit confused about why there is a problem: why use SG numbers? P 2
21 21 (or indeed P22121) is clear and unambiguous. There is no need to use
the numbers (and certainly not the weird CCP4 numbers like 3018 which I was
trying to hide in Pointless
Phil
On 2 Oct 2014, at 15:04, Kay
On 2 October 2014 13:51, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I don't see any sticking to initial indexing as worthwhile to worry
about, since in the first integration, P1 is often used anyway, and it is
quite normal (and easy) to re-index after the intensities become
Hi Phil,
as far as I understand, you are stating a consensus (do not use
numbers, do use the Hermann-Mauguin-symbols), rather than a problem. The
problem seems that the artificial space group numbers 1018, etc.,
contained in symop.lib, do not follow the consensus and thus cause
irritation.
Best,
How can it be if you're not even sure what the correct space group is?
Ambiguities may arise in the presence of pseudosymmetry and/or packing
disorders. In some cases, you can determine crystal structure from the
same data in different space groups that do not have subgroup/supergroup
On Thu, 2 Oct 2014 16:00:30 +0100, Ian Tickle ianj...@gmail.com wrote:
On 2 October 2014 13:51, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I don't see any sticking to initial indexing as worthwhile to worry
about, since in the first integration, P1 is often used anyway, and it is
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
Look at $CLIBD/syminfo.lib
All listed by number as well as other flags..
Eleanor
On 30 September 2014 13:17, Philip Kiser p...@case.edu wrote:
From XDS:
** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY **
BRAVAIS-POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
TYPE
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 abc
The space group names are
Hi all,
Thanks for your help.
CORRECT.LP includes precisely the information I was after.
Also Ian Tickle’s article on http://www.ccp4.ac.uk/html/alternate_origins.html
is very helpful.
Simon
26 matches
Mail list logo
