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The DRAW command allows a user to draw a molecule under the control of either one of two plotting programs. The command will produce files which can then be read by the MOLD or PLT2 plotting programs, which actually prepare the drawing. CONGEN also has a command for making space filling drawings of a molecule, see section Sphere Drawing -- CPK Style Molecular Graphics.
The program, PLT2, is provided as a support program, see
section Support Programs. MOLD is an obsolete program, and is only available
on backup tapes from Harvard.
When using PLT2, in addition to plotting the molecule, one can also plot atomic properties in a table on the molecule as well. One can either represent scalar quantities by varying the size of the circle drawn for each atom, or one can represent vector quantities by drawing vectors attached to each atom.
When using either plotting program, it is also possible to draw a portion of the molecule or only selected atoms. The commands for deleting data from the table are used to delete atoms from an atom table. This table is then used to determine which atoms should be plotted. When atoms are deleted, one can specify an option to this command causing it to relink all atoms which previous had a chain of bonds connecting them.
DRAW [COMPARE] [CONNECT] [TABLE]
[MOLD ATOMU unit BONDU unit ]
[ ]
[PLT2 [SCALAR prop del ] ]
[ [VECTOR [CENTER] prop del prop del prop del del] ]
[ ]
[ [RADII [IUPAC] repeat({atom-type} real) del] ]
[ { ALL } ]
[ ]
[ [LABEL [IUPAC word] [FREQ int] [HEIGHT real] NAME del] ]
[ [GLASS] ]
[ [NOFR] ]
[ [SCALE real] ]
[ [HBOND [DASH int] ]
[ [SIMDASH int] ]
[ UNIT unit] ]
The COMPARE option specifies that the comparison data structures should be used for the drawing. Leaving this option causes the main structure to be used.
The TABLE option specifies that the table should be consulted to see which atoms should be plotted. In the absence of references to the table via the SCALAR or VECTOR options, the entire molecule will be plotted. However, when this option is present or when the table is referenced, the table must be an atom table, and only those atoms which are in the table will be plotted.
The CONNECT option causes the command to reconnect bonds which link atoms that are not be drawn, i.e. deleted atoms. Normally, if an atom is not drawn, any bonds to that atom are not drawn either. However, this is not always satisfactory. For example, if one wants an alpha carbon plot, one wants all the alpha carbons drawn with bonds provided they were in the same chain.
The algorithm used by the connect algorithm is simple, but it can yield strange results in certain circumstances. If a deleted atom has only one bond going to it, the bond is deleted. If it has two bonds going to it, the two atoms are bonded to each other except if they are already bonded to each other. If there are multiple bonds, then all the atoms linked to the deleted atom are rebound into a cycle. One example where this algorithm doesn't work best is if only the gamma carbon of phenylalanine is deleted. In this case, a triangle will be drawn connecting C-beta, C-delta-1, and C-delta-2.
To generate MOLD files, one must specify MOLD and the ATOMU and BONDU operands. These give the unit numbers where the atomic coordinates and bonds are written, respectively.
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 section 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.
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