 |
 |
That is perfectly clear. What was confusing me was indeed (mostly) the PDB CRYST1 record. I guess I will go for R32:h. Thanks a lot, ciao, s On Jul 30, 2012, at 6:36 PM, Ian Tickle wrote: > 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] >> >> >> >> >> >> >> -- 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]