Not knowing enough about what x, 1/2-y, 1/2+z really means, I would load a modified CIF file that only gives that particular operator and see what it looks like.
Bob is right of course :-) Pat should be using CIF files rather than PDB if he wants to illustrate symmetry on: http://macxray.chem.upenn.edu/cells/ What Pat is doing can readily be achieved using CIF files containing just one molecule plus different symmetry operations. The first CIF file would contain just the molecule and the fundamental symmetry position x,y,z. Then subsequent CIF files would contain the same thing plus additional symmetry operations - this means reloading the whole molecule each time, but the molecule is small anyway.
1st CIF file:
_symmetry_equiv_pos_as_xyz 1 'x, y, z'2nd CIF file:
_symmetry_equiv_pos_as_xyz 1 'x, y, z' 2 'x, 1/2-y, 1/2+z'
etc.
But otherwise it would indeed be interesting to have a Jmol script to apply symmetry operations ie:
Select (Basis);
Symmetry (x, 1/2-y, 1/2+z)
Select (Basis) would mean select all atoms if it is a file that does not contain symmetry operations (PDB, XYZ etc), but select only the atoms whose coordinates are listed if it is a file that can contain symmetry operations (CIF, ShelX etc)
Symmetry (x, 1/2-y, 1/2+z) would mean duplicate this selection after applying this transformation - in this case x is unchanged, y is inverted and 0.5 added, and 0.5 is added to z for all selected atoms.
I have suggested "Basis" (asymmetric unit) rather than "Molecule" because the basis might contain more than one molecule or instead represent only part of a (symmetric) molecule. Actually it would also be useful to be able to select the "Basis" associated with a particular symmetry operation, 1,2,3 etc. That way Pat could load a single CIF file and switch on/off the content generated by the various symmetry operations.
Apart from educational illustration, a "Symmetry" script would allow crystallographers to check for pseudo-symmetry. Many structures are "almost symmetric" or sometimes the crystallographer fails to see that a more symmetric structure might fit his data equally well. A Symmetry script might allow him to visualise the effect of adding additional symmetry. (More useful for CIF/ShelX than PDB).
Alan.
_____________________________________________________________
Dr Alan Hewat, ILL Grenoble,
FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
+33.476.20.72.13 (.26 Mme Guillermet)
http://www.ill.fr/dif/AlanHewat.htm
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