OVERLAY
A Molecular Superposition Program
OVERLAY: A Molecular Superposition Program
This program is used to superimpose two chemically identical sections within a molecule or in two different molecules. To use this program one first specifies a target with the TARGET statement. The target is a portion of the structure which will not be moved while other sections of the structure are placed on top of it. The target may be either a single residue or a residue range. Only the atoms within each residue whose names are on the SELECT statement will be used to determine the match. A SELECT statement must always be given and all the atoms on the SELECT statement must be in each of the residues mentioned on both the TARGET and OVERLAY statements.
The command OVERLAY is used to specify a residue or residue range for which a rotation matrix and translation vector will be calculated (Kabsch, W., Acta Cryst. (1978). A34, 827-828). The OVERLAY command does not apply this transformation to anything, it simply is remembered. The APPLY command is used to ask the program to apply the transformation to a specified portion of the structure. The portion may either be a residue, or a list of wild cards. The PUNCH command causes the new coordinate set to be printed to the specified file in the desired format. The PUNCH command can also be used to print the transformation itself to a file.
This program will accept and apply transformations defined with the TRANSFORMATION statement. The TRANSFORMATION statement will accept Euler angles, spherical polar angles, or a raw matrix. When multiple OVERLAY and TRANSFORMATION statements are encountered the most recent is used by the APPLY and PUNCH commands.
The program can also RENAME a chain or chain type, or COPY a collection of atoms to a new chain. These commands allow a great deal of flexibility in the operation of this program. With the RENAME command one can read two structures which originally had the same chain name and then superimpose them.