Symmetry Operations

Symmetry Operations

 

lstsymm

 

Prints symmetry operations and their codes for current structure.

envi

[r=2.7 Å] A1 or one selected atom [-h] [-q]

Note: if more than one atom is selected the first one is used

Prints a list of those atoms within a sphere of radius r around the specified atom.

  • -h: adds hydrogen atoms to the list
  • -q: option adds Q-peaks to the list

 

mode

grow [-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 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)
  • -r: shows directions to all symmetry equivalent atoms 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 immediately attached to that bond is grow, if the atom with outgoing 'grow' bonds is clicked - atoms for all bonds are grown

mode

pack

Displays the position of symmetry equivalent asymmetric units as tetrahedra. These asymmetric units can be generated by clicking on the corresponding tetrahedron.

sgen

atoms

The Symmetry operation is represented as 1_555, 1555 or -1+X,Y,Z and atoms as a selection or a names list

Generates symmetry equivalents of the provided (or all atoms, if there is no selection) using the provided symmetry operation.

Note: For symmetry operations starting with '-' and letter, a leading zero must be added, for example, 0-x,-y,-z, otherwise Olex2 confuses this with an option.

pack

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

Example: pack $O will pack all O atoms with the default of -1.5 to 1.5 cells range.

pack

from to

Equivalent to 'pack from to from to from to', like 'pack 0 1' is expanded to 'pack 0 1 0 1 0 1'

pack

cell

Shows content of the unit cell. In conjunction with 'grow -w' allows the creation of views where all asymmetric units contributing to the unit cell are shown.

pack

r

Packs fragments within radius r of the selected atom(s) or the centre of gravity of the asymmetric unit.

grow

[atoms] [-w]

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 symmetry previously used operations to other fragments of the asymmetric unit

Example: If the main molecule is grown, but only one solvent molecule is shown, using 'grow -w' will produce other solvent molecules using symmetry operators used to grow the main molecule

If some atoms are deleted after growing operations, Olex2 will use existing unique atoms as the asymmetric unit atoms; this can be helpful to avoid a sequence of sgen/kill commands.

labels -l -i: Adds labels only to the 'original' - i.e. not created by symmetry - molecule.

In a packed structure: Right-click on a bond > Graphics > Select the Groups(s): Will select all bonds (or atoms) of that type in the grown structure.
 

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