otfbs: generate ball-and-stick style diagram in PostScript

Otfbs takes a PDB file, as output by a program such as midas, and generates a ball-and-stick image of the atoms and bonds using PostScript. The output of otfbs may be sent directly to a PostScript printer. Alternatively, otfbs can generate Encapsulated PostScript files that may be incorporated into documents.

Otfbs interprets not only the standard PDB format records, but also ``USER'' records of the appropriate format. Any USER record that begins with the words EYEPOS, WINDOW, CHAIN, COLOR, or RADIUS is also interpreted specially. For details of this format, see the PDBRUN format description in the Midas User's Manual.

Command Line Usage

otfbs [ -b ball_fraction ] [ -e ] [ -f ] [ -m margin ] [ -s stick_fraction ] [ -F fill_type ] [ PDBRUN-file ]

The command line flags interpreted by otfbs are:

-b ball_fraction: Set the radius of the rendered circle to be ball_fraction the radius of the atom. The default value is 0.25.
-e: Generate Encapsulated PostScript. Normally the image is automatically scaled to fit an 8.5x11 page with one inch borders. When this flag is given, the image is scaled to fit in a 3-inch square.
-f: Put a frame around the displayed image.
-m margin: Set the margin between the image bounding box and the edge of the page. This margin is only present when the -e flag is absent. The margin is given in PostScript units (i.e., 72 units per inch), and is 2 by default.
-s stick_fraction: Set the width of the rendered stick to be stick_fraction the radius of the rendered circles. The default value is 0.5.
-F fill_type: Normally, the circles and sticks drawn by otfbs are figure outlines. If the fill_type string contains an `b' or `B', the balls will be drawn as filled circles. If the fill_type string contains a `s' or `S', the sticks will be drawn as filled sticks.

Bugs

Otfbs requires that USER records specifying EYEPOS and WINDOW be present in the input file. These records are automatically supplied by midas(1), but are not simple to compute manually.