label3d - Raster3D package

# LABEL3D

#### SYNOPSIS

label3d is a shell script that processes a Raster3D input file containing label descriptors (object types 10, 11, 12) into a TIFF or PNG image containing both the molecular graphics image and the associated labels.

    label3d [-png  [outfile.png]] < infile.r3d   [ > outfile.png  ]
    label3d  -tiff [outfile.tiff  < infile.r3d   [ > outfile.tiff ]

The syntax of the label3d command in version 2.6d has been changed to match that of the render command. Input is from stdin, output is to stdout unless given explicitly as a parameter to the -tiff or -png switches.

Unfortunately, the Raster3D render program cannot process labels. To overcome this lack, earlier Raster3D distributions included an auxilliary program r3dtops that complements render in that it can process the labels but not the graphics objects. The r3dtops code is now part of the render program itself, and is invoked if the -labels command line switch is present. In this case the labels are converted to PostScript commands and placed in a file label3d.ps. The label3d script automates the process of rendering the image, running the resulting PostScript file through ghostscript, and then recombining the two component images into a single TIFF or PNG image containing both the molecular graphics objects and the associated labels.

#### EXAMPLE

Example 7 (figure at right) in the Raster3D distribution illustrates the use of the label3d script. The example script actually produces a stereo pair that shows labels positioned in three dimensions.

#### ENVIRONMENT

The script creates scratch files in directory $TMPDIR, if defined, otherwise in /usr/tmp. PostScript fonts are scaled by the environmental variable FONTSCALE. FONTSCALE = 3.0 yields rendered fonts that approximately match their nominal point size when printed on a 300 dpi printer. For images to be viewed on a video monitor, FONTSCALE should be set to something close to 1.

The label3d script requires the ImageMagick image processing package, and ghostscript.

#### BUGS

- The whole nature of label handling in Raster3D is not yet settled. It would be much nicer if all the label processing were taken care of by the render program itself.

- Labels always appear on top of the molecular graphics image, even labels which should be occluded by a foreground object.

#### AUTHORS

Ethan A Merritt.

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