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 <ber...@upstate.edu> 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<hofkristall...@gmail.com> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>>> Theresa Hsu >>>> Sent: Friday, July 27, 2012 12:54 PM >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> 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! sebastiano.pasqual...@ieo.eu
