CONVERT: Command Statements
ADD {XYZ | B | OCC} {<Value> | <Value> <Value> <Value>}
This command is used to add a constant to a particular type of parameter for each atom in the structure. When the XYZ parameters are to be affected three values must be given to define the translation vector. When either temperature factors (B's) or occupancies (OCC's) are specified a single number is given. In any case the number read from the statement is added to each parameter of the indicated type in the model. For instance this command may be used to change the average temperature factor of a model.
No B factor or occupancy can be moved outside the values imposed by the most recent RANGE statement.
This operation would be performed with a statement looking like
JIGGLE {XYZ | B | OCC} <RMS value>
This command adds a random value to the parameter class specified. The amount of distortion is normally distributed with the r.m.s. value specified by the user. The values allowed for B or OCC parameters are be restricted to a particular range by the most recent RANGE statement. By default B factors will lie between 1.0 and 100.0 while OCC parameters will be restricted to values between 0.0 and 1.0.
Some example statements are given here.
The first example mangles the XYZ parameters of the model with an r.m.s. value of 1.0. The second example adds an r.m.s. variation of 5.0 to the B factors.
PUNCH <File name> {ATOM | ATOMC | ATOMG | SEQUENCE | CELL |
AMSOM | PDB | DIAMOND |
DSN2 | HENDRICKSON} -
N(<Atom type code> <Atom type name>)
This command writes out all atoms presently known to the program to the named file in the format specified.
A CELL statement is required to convert to Diamond, DSN2, Hendrickson, or PDB formats. DSN2 file conversion also requires the symmetry operators of the space group.
If Amsom, PDB, Diamond, DSN2, or Hendrickson format is desired, the sequence file for the structure must have been supplied. If a SEQUENCE file is desired, a sequence must be entered, either by giving a sequence file (the null operation), or a PDB, Diamond, DSN2, or Hendrickson formatted file.
One would want to PUNCH a file of CELL format when converting from a PDB format file. The cell constants are usually stored in the PDB file. One can PUNCH these values in a file which contains only a CELL statement. This file can be INCLUDEd when other TNT programs read the new coordinate file.
Here are some examples.
The coordinate system of the Diamond file produced is crystallographic Ångstroms (fractional times cell edges). This coordinate system is the only one that can be produced in a Diamond file with Convert.