The most overloaded command in Olex2! You need to know about this…
  • 155: all symmetry generated atoms currently shown, which were generated by the given symmetry operation.
  • rings NC5: all pyridine rings
  • fvar -2: atoms where a parameter is linked to FVAR 2
  • part 1: all atoms in PART 1
  • isot: all isotropic atoms
  • frag C5: the whole fragment containing C5
  • $E: all atoms of the given type. E is a chemical element symbol or one of the following: * - all types, M - all metals, X - all halogens
  • $*,E: all atoms, but of the E type.
  • $*,H: all non-H atoms
  • wbox: Shows the 3D selection box constructed for all/selected atoms. This box can be used to pack the structure or to crop the voids display/electron density maps. If the third argument (cell) is provided, the frame gets the dimensions of the unit cell rather than being rectangular (this box can be used for packing and 3D maps trimming/extending).
  • ofile n: selects all atoms in the overlayed file n; if n is 0, elements of the currently focused file are selected

The command can also be used to set the publication flag automatically for the new CIF (like after re-refining the structure). This can done using ‘sel cif’ followed by ‘bonds’, ‘angles’ or ‘torsions’/‘dihedrals’.

For example:

  • cif bonds $M: this will make all bonds containing a metal selected
  • cif bonds C1 $O: all bonds from C1 to any O atom
  • cif angles $* $M $*: all angles with a metal in the middle