BS(1)

NAME

bs - generate ball-and-stick style diagram in PostScript

SYNOPSIS

bs [ -b ball_fraction ] [ -e ] [ -f ] [ -m margin ] [ -s

stick_fraction ] [ -F fill_type ] [ PDBRUN-file ]

DESCRIPTION

Bs takes a PDB file as output by the midas pdbrun command (with the conect keyword argument), and generates a ball- and-stick image of the atoms and bonds using PostScript. The output of bs may be sent directly to a PostScript printer. Alternatively, bs can generate Encapsulated PostScript files that may be incorporated into documents.

Bs 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 interpreted specially. For details of this format, see the pdbrun format description in the Midas User's Manual.

COMMAND LINE FLAGS

The command line flags interpreted by bs are:

-b ball_fraction

Set the radius of the rendered circle to be ball_fraction of 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 and its bounding box. 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 radius of the rendered stick to be stick_fraction of the radius of the rendered circles. The default value is 0.5. Stick_fraction must be between 0.0 and 1.0 (exclusive).

-F fill_type

Normally, the circles and sticks drawn by bs are figure outlines. If the fill_type string contains an `a' or `A,' the atoms will be drawn as filled circles. If the fill_type string contains a `b' or `B', the bonds will be drawn as filled sticks.

EXAMPLES

     From MIDAS, the command to print a bs figure with a
     surrounding frame would be:
          pdbrun conect bs -f | lpr -Pprintername

     The command to save an Encapsulated PostScript bs image to a
     file would be:
          pdbrun conect bs -e > savefilename

BUGS

Bs 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.

SEE ALSO

midas(1)

AUTHORS

Conrad Huang

UCSF Computer Graphics Laboratory