Prints symmetry operations and their codes for the current structure.
[r=2.7 Å] A1 or selected atom [-h] [-q]
Prints a list of those atoms within a sphere of radius r around the specified atom. If more than one atom is selected, the one that was selected first is used.
- -h: adds hydrogen atoms to the list
- -q: adds Q-peaks to the list
[-s] [-v] [-b] [-shells]
Displays the directions in which the molecule can be grown.
- -s: also shows the short interaction directions.
- -v: [2.0 Å] shows directions to the molecules within the v value of the Van der Waals radii of the selected atoms, which can be generated by clicking on the direction representations. Only unique symmetry operations (producing shortest contacts) are displayed. If an atom is selected before entering this mode, the environment of only this atom(s) can be grown.
- -r: shows “growing bonds” to symmetry equivalent atoms of the selected one(s) within 15 Å. Shortcut CTRL+G is used to enter the ‘mode grow’
- -shells: only applicable in
>>mode grow -shells- allows growing atom by atom. If a ‘grow’ bond is clicked, only the immediate attached to that bond atom is grow, if the atom with outgoing ‘grow’ bonds is clicked - atoms for all bonds are grown
Displays the position of symmetry equivalent asymmetric units as tetrahedra. These asymmetric units can be generated by clicking on the corresponding tetrahedron.
Generates symmetry equivalents of the selected atoms (or all atoms, if there is no selection) using the provided symmetry operation. Note: For symmetry operations starting with
-and a letter, a leading zero must be added or the expression has to be quoted (for example,
0-x,-y,-z), otherwise Olex2 confuses this with an option. The Symmetry operation is represented as
-1+X,Y,Zand atoms as a selection or a names list. As a special case, twelve numbers can be provided to specify any matrix operating on the fractional coordinates (e.g. see the match)
a_from a_to b_from b_to c_from c_to [atoms]
Packs all or specified atoms within given dimensions.
- -c: prevents clearing existing model.
>>pack $Owill pack all O atoms with the default of -1.5 to 1.5 cells range.
pack from to from to from to, like
>>pack 0 1is expanded to
pack 0 1 0 1 0 1
Shows content of the unit cell. In conjunction with
>>grow -w, it allows the creation of views where all asymmetric units contributing to the unit cell are shown.
Packs the volume of the structure inside a 3D selection box. You can select 3 atoms and type
>>sel wboxto create a box around just that part of the structure. To keep already shown box around atoms and work on another part of the structure, use the $-c$ option.
Packs fragments within radius r of the selected atom(s) or the centre of gravity of the asymmetric unit.
[atoms] [-w] [-s]
Grows all possible/given atoms. For polymeric structures or structures that require to be grown several times, Olex2 will continue grow until the operation results in a symmetry element that has been used previously.
- -w*: permits the application of previously used symmetry operations to other fragments of the asymmetric unit. In other words: if parts of the structure have been grown, this command will also generate symmetry equivalent atoms that are not connected to the already grown fragment, i.e. solvent molecules.
If the main molecule is grown, but only one solvent molecule is shown, using
>>grow -wwill produce other solvent molecules using symmetry operators used to grow the main molecule.