SYMMETRY applies crystal SYMMETRY operations on given SELECTIONS of atoms. The cell constants and symmetry operations in the form of international tables or from a density map should be read before. Each additional SYMMETRY operation applied results in a new segment which name begins with '#'.
SYMMETRY SELECT ... END NEIGHBOUR inte RESIDUE DISTANCE real (15.0) CUT real MATRIX inte TRANSLATION inte inte inte CELL AROUND SELECT ... END CENTER * DELETE ON / TRUE OFF / FALSE
... SELECT ... END ...
... CELL ...
CELL applies each SYMMETRY operation only once. The atomic coordinates are afterwards converted so, that they are placed into 1 cell only. (Their fractional coordinates can only have values between 0.0 and 1.0.) However, the resulting coordinates are, as by other options, in cartesian coordinate system.
... NEIGHBOUR inte
NEIGHBOUR integer specifies how many neighbour layers (inte) of molecules should be created from each crystal symmetry molecule. Each molecule is translated for inte times for a cell length in the crystal lattice in all 6 directions. All together 26 additional structures are created when integer is 1. Do not use more than 1 for proteins unless you really know what you are doing.
The RESIDUE command word turns a flag, that disables copying of RESIDUE structure into the newly created SEGMENT, so that each newly created segment is a single RESIDUE only. It should be used for crystal packing studies, otherwise the residue number goes quickly over the array boundaries.
... DISTANCE real
The 'DISTANCE real' specifies how close should some the box inside which by symmetry operations generated molecules comes to the AROUND boundaries. When CUT is turned on, then the DISTANCE is explicitly checked for each particular atom. The default value is 15.0A.
... CUT real
CUT is a flag, that enables the DISTANCE checking of each particular atom. Each generated atom should be closer than the specified DISTANCE AROUND the CENTER or any atom in the AROUND SELECTION.
... MATRIX inte
Applies only the specified crystal rotation MATRIX.
... TRANSLATE inte inte inte
Applies beside the crystal symmetry operation explicitly only the specified TRANSLATION. The NEIGHBOUR option is DISABLED.
... AROUND SELECT ... END ... CENTER * (see syntax at image center)
Creates symmetry related atoms from the first SELECTION around the AROUND SELECTION of atoms.
Specifies the CENTER around which symmetry related atoms will be generated.
The CENTER option defers from the SELECT option since it automaticaly assumes the CUT and DELETE ON option. It is also computationally faster, however it can not generate atoms AROUND a nonspherical shape. The CENTER option is supposed to be used during an interactive model building session. The RESIDUE information can not be suppressed as well.
... DELETE ON OFF
DELETES when the DELETE flag is ON or TRUE, the symmetry related atoms generated by the identity crystal symmetry operation (X,Y,Z) with no additional translation. When the DELETE flag is OFF or FALSE, the atoms are not deleted. OFF is the default. It should be used for generation of symmetry environment while building the residues in to the electron density.
MAIN> symmetry select all end neigh 1 around select sequence 57 end - MAIN> distance 20. cut delete on
MAIN> key old select all end MAIN> symmetry select numb segment 1 end neigh 1 around select napa end - MAIN> distance 20. cut delete on MAIN> key sym1 select .not old end MAIN> key old select all end MAIN> symmetry select numb segment 2 end neigh 1 around select napa end - MAIN> distance 20. cut delete on MAIN> key sym2 select .not old end MAIN> key old select all end MAIN> symmetry select numb segment 3 end neigh 1 around select napa end - MAIN> distance 20. cut delete on MAIN> key sym3 select .not old end MAIN> key old select all end
MAIN> symmetry select ca end neigh 1 around select ca end - MAIN> distance 50.0 residue