Hi Sebastiano

How programs refer to it is irrelevant for the purposes of
publication!  If you want to be precise and stick to the ITC
convention on nomenclature it's "space group R32 in the setting
R32:h", since as I explained it's only the standard symbol R32 which
is generally shown in the main ITC table of space groups; the setting
symbols are not shown in all cases.  However simply calling it 'R32:h'
is also completely unambiguous and acceptable (but calling it 'R32'
most definitely is not!).  For the PDB CRYST1 record you have
(unfortunately) to call it 'H32'.

Hope this clears it up.

-- Ian

On 30 July 2012 17:20, Sebastiano Pasqualato
<[log in to unmask]> wrote:

Hi there,

at this point I'm confused, at least with respect to one thing.

If I have a solved a structure in spacegroup #155, with a=b and different

from c, and alpha=beta=90, gamma=120, this would be reported as R32 in the

international tables. However programs refers to it as H32.

What should I report in the (in)famous  "table 1" ?

Thanks in advance,

ciao,

s

On Jul 30, 2012, at 5:23 PM, Ian Tickle wrote:

Without wishing to re-ignite previous discussions on this topic

(perhaps <FLAME> ... </FLAME> tags would be in order!), I would point

out that this and similar confusion with other space groups has arisen

largely from a failure of some programmers (and users!) to fully

comprehend the important difference between a 'standard symbol' and a

'setting symbol' for a space group, no doubt because in many cases

these are superficially identical, or a least very similar.  This

point is also made in the Computational Crystallography Newsletter

article on H3 and H32 that I referenced earlier.

The Hermann-Mauguin symbol (aka 'standard symbol') is unique to a

space group and crucially is designed to be independent of the setting

(orientation and/or origin).  It is used to identify a space group

without reference to the setting, and therefore its main use is to

provide page headings and index entries in ITC. There exist exactly

230 H-M standard symbols for the 230 unique 3D space groups.  The H-M

standard symbol is the same for all settings of a particular space

group and therefore cannot be used to define the setting: for that you

obviously need additional information.

The standard symbol is thus of little or no relevance to practical

crystallography: for that you must use a setting symbol.  However for

the majority of space groups only one setting is accepted as

'conventional' so in those cases the standard and setting symbols are

identical; it's only where there are multiple settings that problems

arise.

A simple analogy might be to say that an object is called 'building'

and that is also its standard symbol.  It describes the object without

reference to its orientation or position and so is not relevant to the

practical problem of defining the view of the building: for that you

need extra symbols.  For example you might need to specify one of the

setting symbols 'building (front elevation)', 'building (side

elevation)' or 'building (plan)'.

So R32 is a H-M standard symbol which corresponds to the 2 alternate

setting symbols R32:r and R32:h as described in the article.  Plainly

you can't use the H-M symbol R32 to uniquely specify the setting since

it is the standard symbol for both the R32:r and R32:h settings.  The

latter are _not_ H-M symbols: they are ITC extensions of the H-M

symbol.

For other space groups further confusion has arisen because ITC often

uses the exact same character string for both the standard symbol and

one of the corresponding alternate setting symbols.  An obvious

example is P21212: this is the H-M standard symbol for SG #18 but is

also one of the 3 ITC setting symbols for P21212, the other two being

P22121 and P21221.  Perhaps the intention would have been clearer if

the ITC setting symbols had all been made different from the standard

symbol, as they are in the R32 case.  For example P21212a, P21212b and

P21212c would have been equally valid choices for the ITC setting

symbols but do not express a 'preferred' setting (since there isn't

one).  Similarly the standard symbol for SG #5 (unique axis b) is C2,

and the alternate setting symbols are A2, C2 and I2, but they could

equally well have been (for example) C2a, C2c and C2i, which doesn't

express a preference for any one of the alternate settings.

Either way, according to the ITC rules, the choice of 'conventional'

setting for a space group (i.e. the recommended default choice when

there are no other grounds such as isomorphism with a previously

determined structure) is made by reference to the unit cell.  For R32

the conventional cell happens to be the hexagonal one (a = b != c,

alpha = beta = 90, gamma = 120) with symbol R32:h; for all

orthorhombic SGs the convention is a < b < c and the setting symbol

derives from that.

Cheers

-- Ian

On 28 July 2012 22:22, Edward A. Berry <[log in to unmask]> wrote:

Are all the software packages consistent in their (mis)use of these

symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3,

and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to

be).

Ian Tickle wrote:

If we're all agreed that ITC(A) is taken as the authority on all

matters of space group symbology (and I for one certainly agree that

it should be), then SG symbol H32 (SG #145:

http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do

with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)!

According to the Hermann-Mauguin system of nomenclature H32 (more

correctly written as H3_2 where the '_' indicates a subscripted screw

axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2

in H-M).  H32 as an alternate setting symbol for R32 is a very recent

PDB invention which conflicts with the well-established H-M convention

used throughout ITC.  The ITC symbols for the rhombohedral&  hexagonal

axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious

extensions of the H-M symbols without introducing any conflict with

the existing convention, as the PDB symbol does.  The confusion has

arisen from the failure to distinguish the lattice type (the first

letter of the symbol) from the symbol for the basis system of the

setting (the final letter after the ':').

See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an

excellent explanation of all this and of the confusion that arises

when programmers ignore established conventions and 're-invent the

wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols

R32&  H32 and uses R32 for PDB H32 and vice-versa!).

Cheers

-- Ian

On 27 July 2012 21:09, Bernhard Rupp<[log in to unmask]>  wrote:

H32 indicates the hexagonal obverse setting (as you list) for a R

centered trigonal cell, which is 3x larger than the primitive R32 cell

indexed a=b=c, al=be=ga<>  90. Standard imho is the H32 setting, for which I

will probably get flamed.

The relation between H and R cells is depicted here:

http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm

This has been discussed and is explained in the ccp4 tutorials and doc

afaik, where you can find more detailed info.

For proper format in a journal, I would suggest to adhere to the format

given in the ITC (International tables for Crystallography), I.e. Bravais

Italic, subscripted screw symbols. Note that this is not the format you put

it into most programs - their docs help.

You can also try my old space croup decoding program to see general

positions, operators, matrices and other useful stuff.

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

HTH, BR

-----Original Message-----

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of

Theresa Hsu

Sent: Friday, July 27, 2012 12:54 PM

To: [log in to unmask]

Subject: [ccp4bb] Space group R32 and H32

Dear all

I have a confusion on the space group R32 and H32. For a cell parameter

of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as

R32 or H32?

I tried searching the mail list archives but it does not help a beginner

crystallographer like me.

I also have another basic question. What is the correct way for writing

space groups? Is the Bravais lattice in italic and is there space after

that? Or it does not matter because both are used in literature?

Thank you.

--

Sebastiano Pasqualato, PhD

Crystallography Unit

Department of Experimental Oncology

European Institute of Oncology

IFOM-IEO Campus

via Adamello, 16

20139 - Milano

Italy

tel +39 02 9437 5167

fax +39 02 9437 5990

please note the change in email address!

[log in to unmask]