The Symmetry major menu implements the application of crystallographic symmetry to a molecule. This requires that entries exist in the database for the unit cell and the symmetry operators of the space group of the molecule. These can be added via Read_formatted or by the Symm_setup commands
The Symm_sphere command generates complete molecules for the symmetry related molecules. Their names are generated from user supplied names. After a call to Symm_sphere the molecules exist in the database as molecules in their own right, until overwritten by a later call or deleted by the user. The user may like to paint carbons a different colour to make the symmetry atoms easier to recognise.
If the asymmetric unit contains more then one chain, and these exist as separate molecules in the database, then a number of symmetry commands may be necessary to show all neighboring molecules.
Symm_setup <mol> <cell> <symmops>
Setup for symmetry. The user is prompted for the molecule name, the unit cell constants, and then a formatted text datablock describing the crystallographic symmetry operators. This datablock must be named '.space_group_operators' and must contain an explicit description of ALL symmetry operators (including centred ones). The unit transformation operator must be the first one defined.
As everywhere else in O, each operator consists of 12 floating point numbers,
encoding a rotation matrix and a translation matrix. The rotation matrix Rij is a 3x3 matrix while the translation matrix Ti is a column vector. They MUST be stored in columns as R11, R21, R31, R12, R22, R32, R13, R23, R33, T1, T2, T3. The operators for space group P21 would be 1. 0. 0. 0. 1. 0. 0. 0. 1. 0. 0. 0. , followed by -1. 0. 0. 0. 1. 0. 0. 0. -1. 0. 0.5 0. . Examples for the common space groups are found in the data directory.
This option creates 2 datablocks, <mol>_cell and <mol>_symmop.
Symm_sphere <mol> <symm_mol_name> <radius>.
Draw all symmetry related atoms within a sphere of given radius, centred on the .active_centre . Each symmetry operation that is found, generates a complete molecule in the database and a separate object of the part within the sphere. The names of the new 'symmetry molecules' are derived from the supplied <symm. mol. name>.
Symm_object <molecular object> <symmetry object> <radius>
Draw a set of objects that are symmetry related to the desired molecular object and within the specified distance of the current centre. These objects are drawn in one new object and are merely instances of the desired object. As such they have the same colour as that object.
The option creates 2 datablocks, @symmetry_molecules and .draw_symobj.
Symm_cell
Draw a box representing the unit cell of the current molecule. This command assumes the unit cell is in the data base by a previous symm_setup command. The command create a datablock .cell_odl containing the odl instructions to create the drawing.
1.The necessary symmetry information is added to the database of molecule A27 by the following example
symm_setup a27 96.8 112.3 55.0 90. 90. 90. $ODAT/p212121.o
If the datablock describing your space group does not exist in $ODAT , then use the p212121.o file as an example. Remember to include any centring operators as explicit operations.
2.The following example generates symmetry atoms for molecule A27.
symm_sph a27 sym 10.
Any residue with its centre of gravity 10. from the current screen centre (as defined by .active_centre) will appear on the screen. These may be from a number of different symmetry related molecules. Each object is named after the symmetry molecule's name. The first symmetry molecule would be called SYM1, the next SYM2, etc.
The symm_sphere and symm_object command modifies a datablock @symmetry_molecules