23.4 Operands for PLT2 output.

To generate a plotting command file for PLT2, one specifies the keyword, PLT2. One must also specify the unit where the graphics command file should go using the UNIT operand.

The file which is produced for PLT2 gives commands necessary to draw the molecule. They are ordered into portions so that editing the various parts of the plot is simplified. A CM command with a comment described the portion precedes each portion. At the end of the file is a FR 0 command which empties any plotter buffers and pauses. This FR command can be omitted by the presence of the NOFR command. Each of the commands is written with a format of (1X,A2,2X,nF10.3). With this scheme it is easy to write to postprocessors that will further manipulate the drawing.

To specify that the size of the atoms be proportional to a single property in the table, the SCALAR option is used to specify that property. The size of the circle in Angstroms will be equal to the scale factor specified by the SCALE option times the value of property.

To specify that a vector corresponding to three property values be drawn attached to each atom, the VECTOR option is used. The three properties specified become the X, Y, and Z components of the vector. The units are presumed to be Angstroms. The scale factor specified by the SCALE option is multiplied by the components to get the final length.

In order to control the size of atoms when the SCALAR option is not used, the RADII option is available. With the RADII option, one specifies the radius to be used for an atom with a particular IUPAC name or a particular atom type name. One can also specify the default size to be used. The default size of an atom is normally zero. The IUPAC suboption specifies that IUPAC names are being given, otherwise, parameter type names are being given.

Two labeling possibilities are available. Both of these options are invoked using the LABEL option. The first possibility, which is the default, labels residues by residue number within the segment. The IUPAC suboption specifies the IUPAC name of the atom near where the label will be drawn. If such an atom is not present in the residue or if this option is omitted, the first atom will be used. If this selected atom has been deleted, then the next present atom will be labelled. If no such atom can be found, no label will be drawn. The second possibility is specified using the operand, NAME. Here, all atoms which match the IUPAC suboption are labeled by their IUPAC name. The IUPAC option may have wildcards (see Atom Selection) so that multiple atoms within a residue can be labeled. The frequency of labels is given by the FREQ option. When the residue number in the segment can be evenly divided by FREQ, an attempt will be made to place a label. The default value for FREQ is 10. The height of the label in Angstroms is specified using the HEIGHT option. Its default value is 0.5 Angstroms.

The GLASS option specifies that any vector, either bond vector or property vector, start at a distance of the drawn radius of the atom, i.e. as if the atom were a glass sphere. This generates a slightly more realistic drawing. If the vector is totally contained within atoms, it is not drawn.

The SIMDASH option simulates drawing of dashed lines. Dashed lines are drawn by breaking up the three dimensional bond vectors into smaller pieces. In so doing, stereo plots of the dashed lines look OK. The argument specifies the number of segments used for the lines.

The HBOND option causes hydrogen bonds to be drawn as dashed lines. The bond reconnection is NOT done with these bonds, so if an atom in a hydrogen bond is deleted, it isn't drawn. The number of segments in the dashed lines is given by the DASH suboption. This currently defaults to 3.