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Command Statements

APPLY <Chain name>|<Residue name>:<Atom name>

This command instructs the program to apply the most recent transformation to the specified portion of the structure. Wild cards may be placed in any of the fields. If nothing follows the APPLY keyword the transformation is applied to all of the structure.


COPY <Chain name>|<Residue name>:<Atom name> <Chain name>|

This command copies the atoms specified to the second chain mentioned on the input line. The atoms are not simply moved from one chain to the other, they are replicated. Wild cards may be placed in the <Residue name> or <Atom name> slots. The source chain must exist and the destination chain must not. The sequence of the residues in the new chain is preserved. However, any interchain linkages specified on the CHAIN statement are not copied to the new chain because there is insufficient information to build the new links.


OVERLAY <Chain name>|<Residue 1> - <Residue 2>
OVERLAY <Chain name>|<Residue name>

This command causes the program to calculate the transformation which, when applied to the specified section of the structure will cause it to be superimposed on the target residue range specified on the last TARGET statement. If the number of residues given do not match the number on the TARGET statement or there is not a one-to-one match of atoms in the two residue ranges (after considering all SELECT statements) the program will exit with an error message. At least one SELECT statement is must have been encountered before the OVERLAY command.


PUNCH <File name> {ATOM | ATOMC | ATOMG | TRANSFORMATION}

The PUNCH command causes the program to write the coordinates of the entire structure into the named file in the specified format.

If the TRANSFORMATION format is specified, a TRANSFORMATION statement will be written to the named file. This statement will contain the current transformation in TNT's cartesian Ångstrom coordinate system.


RENAME {CHAIN <Chain name> | CHAIN_TYPE <Chain type>} -
                                           TO <New name>

This statement causes the name of the specified chain or chain type to be changed to the value specified. This sort of operation is useful when one wants to compare two structures but both structures are defined using the ``chain with no name''. The first structure can be read, its chain name changed, and then the second structure can be read.

tabular1131

This example shows how a structure, defined with the default chain can be renamed so that both the chain type and chain name is 157I. (In cases where the chain name and type are unnamed, as is usually done when there is only one chain, you can reference the unnamed object with the name ``null".

The RENAME command can rename several other kinds of things as well. For the full details see page gif.


next up previous contents index
Next: Program Operation Up: OVERLAY Previous: Unique Input Statements

Dale Edwin Tronrud
Thu Jul 6 23:24:57 PDT 2000