No that surely can't be right. Application of a symmetry operator to a point on a special position which is unchanged by the operator doesn't generate a symmetry copy of the point, because there is no symmetry copy of such a point! For general Wyckoff positions it does, for sure. If you look at the entry for R3 (hexagonal or rhombohedral setting, it doesn't matter which) on the Wyckoff position website I indicated earlier, you'll see a column labelled 'multiplicity' which is 3 for the general position and 1 for the special position. This means that the symmetry operator generates 3 symmetry copies of a general position (including the original), but only 1 copy (i.e. only the original) of the special positions on the 3-fold.
That's precisely why such points are called "special positions" - i.e. you have to treat them specially! If what you describe is what the refinement program or whatever is doing then it would imply there's a programming error, i.e. the program is not treating special positions as special, it's treating them instead as general positions. As I said whenever you see fractional occupancy reported it should imply some kind of disorder, i.e. the atom exists on that site in only the indicated fraction of the unit cells in the lattice. -- Ian On Fri, Dec 10, 2010 at 10:02 PM, Sue Roberts <s...@email.arizona.edu> wrote: > Hi Ian > > No disorder is involved. > > The occupancy of an (fully occupied) atom on an n-fold rotation axis is 1/n > If a two-fold, 1/2 > If a three-fold, 1/3 > > When you sum over all the atoms in the unit cell, application of the symmetry > operations to atoms lying on the rotation axis generates atoms with unchanged > coordinates. Hence to generate a fully occupied atom on a n-fold symmetry > axis, the original occupancy has to be 1/n. > > Sue > > On Dec 10, 2010, at 2:53 PM, Ian Tickle wrote: > >> Good point Colin! 2-Zn insulin is of course a classic example of >> this, where the two independent Zn2+ ions both sit on the >> crystallographic 3-fold in R3. It doesn't matter whether you count >> the metal ion as part of the protein or not: if I understand Gloria's >> original question correctly, all that matters is that the atom/ion is >> present in the crystal structure. >> >> In fact here are some extracts from the PDB entry (4INS): >> >> REMARK 375 ZN ZN B 31 LIES ON A SPECIAL POSITION. >> REMARK 375 ZN ZN D 31 LIES ON A SPECIAL POSITION. >> REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. >> REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. >> REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. >> REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. >> REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. >> >> HETATM 835 ZN ZN B 31 -0.002 -0.004 7.891 0.33 10.40 >> ZN >> HETATM 836 ZN ZN D 31 0.000 0.000 -8.039 0.33 11.00 >> ZN >> HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 >> O >> etc >> >> Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the >> special position (assuming it's not disordered), though the first Zn >> above and the water do appear to be disordered since they're not >> actually on the special position. Fractional occupancy always implies >> some kind of disorder: occupancy = 1/3 of an atom on a special >> position would imply occupancy disorder, i.e. it's randomly present in >> only 1/3 of the unit cells. >> >> -- Ian >> >> >> On Fri, Dec 10, 2010 at 1:11 PM, Colin Nave <colin.n...@diamond.ac.uk> wrote: >>> Does one regard the metal atom in a metalloprotein as being part of the >>> protein? >>> >>> If so, a shared metal could occupy a special position in a dimer for >>> example. >>> >>> In Acta Cryst. (2008). D64, 257-263 "Metals in proteins: correlation >>> between the metal-ion type, coordination number and the amino-acid residues >>> involved in the coordination" I. Dokmanic, M. Sikic and S. Tomic ( >>> http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are >>> 25 cases of metal atoms in special positions. >>> >>> Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of >>> Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and >>> heme iron in a crystallographic `special position' "D. Cobessi, L.-S. >>> Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( >>> http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the >>> 'special position' is justifiably in quotation marks in this example as >>> disorder is present. >>> >>> Colin >>> >> > > Dr. Sue A. Roberts > Dept. of Chemistry and Biochemistry > University of Arizona > 1041 E. Lowell St., Tucson, AZ 85721 > Phone: 520 621 8171 > s...@email.arizona.edu > http://www.biochem.arizona.edu/xray > > > > > > > > > >
