Command Statements
Here follows a description of the command statements in NCS. Since is would be pointless to run this program if there were no noncrystallographic symmetry the definition of the regions of the model covered by this symmetry is required for all commands. These definitions are made with the CLUSTER statements defined above. The examples given for each command assume that the CLUSTER statements have been placed in the TNT control file yours.tnt. The examples given below presume that the NCS weight and sequence file is also given in the control file.
The SCATTER command requires, in addition, the noncrystallographic symmetry operators, since they cannot be calculated from the unique atoms.
CURVATURE <File name>
This command is used in the long loop of refinement. It causes the function value, and the first and second derivatives of the NCS restraints to be calculated and written to the file specified. This command must be preceded by at least the NCS definition, a coordinate set containing a full set of chains, and a WEIGHT statement. You will need the sequence file if residue ranges are used in the cluster definition.
The noncrystallographic symmetry operators themselves are optional. If they are not supplied NCS will use the current coordinates to derive them.
$tntbin/ncs << $eof INCLUDE yours.tnt INCLUDE init.cor CURVATURE ncs.dat $eof if ($status >< 0) then exit 1
FUNCTION <File name>
This command is used in the short loops of refinement. It causes only the function value for the NCS restraints to be calculated and written to the file specified. This command must be preceded by at least the NCS definition, a coordinate set containing a full set of chains, and a WEIGHT statement. You will need the sequence file if residue ranges are used in the cluster definition.
The noncrystallographic symmetry operators themselves are optional. If they are not supplied NCS will use the current coordinates to derive them.
$tntbin/ncs << $eof INCLUDE yours.tnt INCLUDE shifted.cor FUNCTION ncs.dat $eof if ($status >< 0) then exit 1
GATHER
The GATHER command will average together all the symmetry mates in a noncrystallographic cluster to produce a prototype molecule for each CLUSTER statement. It averages the coordinates, gradients, and curvatures for each atom in each cluster. The unaveraged atoms are then removed from the atom list in the program.
The GATHER command is used when refining a model with noncrystallographic constraints. for example, after Rfactor has calculated the gradient and curvature for the entire cluster (or set of clusters) NCS will move those average values to the prototype's orientation and average them. The averaged gradient and curvature is presented to Shift instead of the originals.
The noncrystallographic symmetry operators themselves are optional. If they are not supplied NCS will use the current coordinates to derive them. Either the operators must be supplied on TRANSFORMATION statements or the coordinates must be given. If both are supplied the TRANSFORMATION statements have precedence.
In the example below, the coordinates from init_expanded.cor and the gradient and curvature from rfactor_expanded.dat are gathered into the CRO prototype using the noncrystallographic symmetry operators from the file cluster.ncs After the gathering the results are PUNCHed to rfactor.dat
The TNT control file is presumed to contain the CLUSTER statement ``CLUSTER CRO CHAINS O A B C". The cluster is named CRO on the CLUSTER statement. init_expanded.cor contains four chains -- O, A, B, and C. rfactor.dat contains only one -- CRO.
$tntbin/ncs << $eof INCLUDE cro.tnt INCLUDE init_expanded.cor INCLUDE rfactor_expanded.cor INCLUDE cluster.ncs GATHER PUNCH rfactor.dat CURVATURE $eof if ($status >< 0) then exit 1
GRADIENT <File name>
This command is used in the long loop of refinement when the method of minimization is to be either steepest descent or conjugate gradient. It causes the function value and gradient for the noncrystallographic symmetry restraints to be calculated and written to the file specified. This command must be preceded by at least the NCS definition, a coordinate set containing a full set of chains, and a WEIGHT statement. You will need the sequence file if residue ranges are used in the cluster definition.
The noncrystallographic symmetry operators themselves are optional. If they are not supplied NCS will use the current coordinates to derive them. If both are given the operators on the TRANSFORMATION statements are used.
$tntbin/ncs << $eof INCLUDE cro.tnt INCLUDE init.cor GRADIENT ncs.dat $eof if ($status >< 0) then exit 1
PUNCH <File name> {ATOM | ATOMC | ATOMG |
GRADIENT | CURVATURE |
NCS}
The PUNCH command is used to get information out of NCS. The actual information produced depends on the format of the file requested.
The program writes a coordinate file with the name and format designated. The command must be preceded by a coordinate set. If ATOM format is used a CELL statement should be given and, in addition, a GRID statement should be given if ATOMG is used.
The program writes the current gradient (and curvature if CURVATURE was specified) to the named file. When applying noncrystallographic symmetry constraints, this command is used after the GATHER command has averaged the gradient and curvature from each individual chain into that of the prototype.
The program writes the full list of noncrystallographic symmetry operators to the file using CLUSTER and TRANSFORMATION statements. If a set of operators were not entered into the program the current coordinates and CLUSTER statements will be used to determine these operators.
SCATTER
This command is used to expand the prototype molecule by the noncrystallographic symmetry operators to generate the entire cluster of molecules. It will expand all occurrences of noncrystallographic symmetry. All of the current information about the atoms of the prototype are expanded: coordinates, gradients, and curvatures. The prototype, itself, will be removed from the list of coordinates.
The noncrystallographic symmetry operators must be supplied to use the SCATTER command, in this example in the file ncs_symmetry.dat. In addition you will need the sequence file if residue ranges are used in the cluster definition.
$tntbin/ncs << $eof INCLUDE cro.tnt INCLUDE shifted.cor INCLUDE ncs_symmetry.dat SCATTER PUNCH shifted_all.cor ATOMC $eof if ($status >< 0) then exit 1
SCREEN <Number>
This command is used to get a list of the worst agreements between the similar chains. It will only consider the regions of similarity defined on the CLUSTER statements. It requires that the NCS definition and a coordinate set be given. You will need the sequence file if residue ranges are used in the cluster definition.
Of course, if you are constraining ncs there will be no deviants to list.
$tntbin/ncs << $eof INCLUDE cro.tnt INCLUDE shifted.cor SCREEN 20 $eof if ($status >< 0) then exit 1