COMBINE <Parameter code> N(<Atom code>)
This statement creates a subset of the structure that will be treated as a rigid body. The positional shifts of each atom in this class are combined so that the relative positions of the atoms within the group are unaffected by the shifts to be applied. Several rigid bodies can be refined simultaneously by entering several COMBINE statements. Each COMBINE statement generates a single rigid body.
The parameter code can be:
The atom code can be either:
<Chain name> | <Residue name> : <Atom name> -- or -- <Chain name> | <Residue 1> - <Residue 2>
In the first case a single atom is specified. If the residue name or atom name slots are left blank they are assumed to be a wild card. If the chain name is left blank it is assumed that the model contains a single chain.
The second form allows the selection of all atoms within a residue range. Both residue names must be given. If the chain name is left blank it is assumed that the model contains a single chain. A space is required before the hyphen (`-').
One may mix and match residue ranges and wild card specifications on the same COMBINE card.
If no atom code is given the parameters of the specified class for all atoms in all chains are combined into a single rigid body.
If non-positional parameters are combined, the shift applied to every atom is the average of the shift that would have been applied to each atom. To force all the atoms in a group to have the same temperature factor or occupancy while allowing the parameter to vary you would first set all the atoms equal to each other and then refine with a COMBINE B or COMBINE OCC along with a description of the group.
The behaviour of COMBINE statements can be modified by setting the MOSES option. By default, any atoms not mentioned on a COMBINE statement is left as a free atom. Mixing rigid bodies and free atoms usually does not work well. When the MOSES option is set all atoms not specifically assigned to a rigid body on a COMBINE statement will be placed in the group it is closest too.
Because of a limitation in the current implementation, COMBINE statements cannot be used along with curvatures. The steepest descent minimization method should be used with rigid body refinement. This is accomplished by giving the third parameter of the tnt command as `sd'. The command would look like ``tnt 1 5 sd''.
CONSTANT <Parameter code> N(<Atom code>)
This statement causes the specified parameters to remain constant.
The qualifiers are as described for COMBINE except that one can specify all the parameters of the atoms (XYZ, B, and OCC) by typing ``ALL''. For example:
The first example fixes the occupancies of all atoms in the structure. The second example fixes all parameters for residues 1 through 316, traced through links, for the default chain. The last statement causes the positions atom SG of residue 1 of chain O and the same atom in chain B to be held constant.
RANGE <Parameter code> <Minimum value> <Maximum value>
This statement sets a limit on the values a particular class of parameters may have. The parameter code must be either B or OCC. The statement need not be used as defaults are provided for the minimum and maximum values of B factors and occupancies. These defaults are 1.0 and 100.0 for B factors and 0.0 and 1.0 for occupancies. If a value is not specified on the RANGE statement the default is used. For example:
In the first example occupancies are allowed to range only from 0.5 to 1.0. The second example allows thermal parameters to range from the default (1.0) to 40.0. The third example allows B's to range from 3.0 to the default upper limit (100.0).