ASSUME RESIDUE_TYPE <Name> WHEN_CONTAINS N(<Name>)
This statement allows you to define a default residue type for any residue which contains all of the atoms listed, and no more. The puddle of water that is contained in most coordinate files presents a continuing maintenance problem in TNT's sequence file. Without the ASSUME statement you would have to edit the sequence file every time you added or removed solvent.
The following example will, I hope, clarify this statement's use. If your model has a great deal of DMSO, instead of creating individual RESIDUE statements for each one you could add to your control file the statement
ASSUME RESIDUE_TYPE DMSO WHEN_CONTAINS S C1 C2 O
Built into TNT is the assumption that a residue which contains only an atom named ``OH" is of type ``HOH". This is the PDB convention for water molecules.
EXCLUDE [<Chain>|]<Residue>[:<Atom>] -
[<Chain>|]<Residue>[:<Atom>]
This statement causes any close contacts between atoms in one group with any atom in the other group to be ignored when deciding what the bad contacts are. A group is defined by giving the chain name, residue name, and atom name of the atom whose contacts are to be ignored.
Wild cards may be placed in any position. The default residue and atom names are wild cards, but the default chain name is the ``chain with no name''. To specify an entire residue one gives the residue name. To specify a particular atom one gives the residue name and the atom name separated by a colon. To specify all atoms with the same name leave the residue name blank and provide a wild card (``*'') as the chain name. Here are some examples.
In the first example all contacts between any atoms in residue 143 with atoms in residue 167 will be ignored. The second example states that if a bad contact is found to exist between atom O of residue 67 and atom O65 of residue SOL1 that contact will be ignored. In the third example the program will ignore all contacts between atoms named O and atoms named C anywhere in the structure.
Here is an example of a use of the EXCLUDE statement which uses the oligomer
definition of Cro given as an example in the ``TNT Sequence File''
chapter (page 
).
EXCLUDE O| O|
EXCLUDE A| A|
EXCLUDE B| B|
EXCLUDE C| C|
These EXCLUDE statements will cause all non-bonded contacts within CRO chains to be ignored leaving only interchain contacts to be listed and refined.