Converting Molscript labels to Raster3D

The most frequent question I get about Raster3D is "How can I get the labels from Molscript into my Raster3D picture?". It actually is possible to do this, but frankly I think it's more effort than the result is worth. I recommend simply labelling your Raster3D output image using an interactive annotation tool on a workstation screen (e.g. the annotate mode of ImageMagick's display program). However, for anyone bound and determined to use Molscript for labelling I will describe how it can be done.

The first thing to do is to establish the size of your eventual image in pixels. Let us say that you want a 3-inch by 2-inch print to be produced on a 300 dpi dye sublimation printer. 300 dpi (dots per inch) times the desired size gives 900x600 pixels for the image size. Construct a header file for the render program which describes this image size; e.g.
```
	My new picture with no anti-aliasing
	 45 30     NTX,NTY number of tiles in x, y
	 20 20     NPX,NPY number of pixels per tile
	     1     anti-aliasing scheme 1 (none)
	 0 0 0     black background
	(etc...)
```
or
```
	My new picture with anti-aliasing
	 45 30     NTX,NTY number of tiles in x, y
	 30 30     NPX,NPY number of pixels per tile
	     3     anti-aliasing scheme 3 (3x3 becomes 2x2)
	 0 0 0     black background
	(etc...)
```
Pay particular attention to the fact (yes, it's confusing) that if you use anti-aliasing schemes 2 or 3 then the eventual number of pixels is not simply the product NTX*NPX,NTY*NPY. This is explained in the render manual.
Now make sure that your Molscript input file is actually drawing in a box of the shape you have just described. To use the procedure I describe below, you must use the "area" command of Molscript to force the lower left corner to (0,0) and the upper right corner to (900,600). Furthermore there must be no bordering frame drawn around the image. So your Molscript input file will begin:
```
	plot
	noframe
	area 0. 0. 900. 600. ;
	background black ;
```
Run Molscript with the -raster3d option to produce an input file to render which uses the header you constructed in step 1.
```
	molscript -r < picture.mol | render | convert avs:- picture.ppm
```
Edit the molscript file to remove or comment out all drawing commands except for the labels. Run molscript again, this time in PostScript mode, to produce a PostScript file containing only the labels.
```
	molscript < picture_labels.mol > labels.ps
```

Use ghostscript to convert the PostScript file into a raster image exactly the same size as your Raster3D image.

	gs -sDEVICE=ppm -sOutputFile=labels.ppm -g900x600 labels.ps

At this point you have two images:

	picture.ppm	900x600 Raster3D image from original Molscript file
	labels.ppm	900x600 image containing only the labels

Use the combine program from ImageMagick to draw the labels on top of the Raster3D image.
```
	combine -compose atop labels.ppm picture.ppm pic+labels.ppm
```
I used the ppm raster file format throughout this example just because it works in both ImageMagick and ghostscript. This may be installation dependent, however. I'll now convert it back to a TIFF file.
```
	convert pic+labels.ppm beautiful.tiff
```
As you see, this is a rather lengthy procedure. Furthermore, the label positioning will be slightly off compared to the pure PostScript version because Raster3D and Molscript treat perspective differently. As I say, I prefer to just type the labels in interactively so that I can see where they are going.

Raster3D homepage

Ethan A Merritt / merritt@u.washington.edu / Biomolecular Structure Center at UW