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New Step 1 Commands


Usually you should not need to change this value, it alters the screening used by the printer. A value of 120 is used by default. On most 300dpi black and white printers this gives much smoother greys than the default used in earlier versions of ALSCRIPT.

PIR_SAVE filename

Will cause the block file to be saved into the file ``filename'' in PIR format. This can be useful for moving block file alignments to other programs.

MSF_SAVE filename

Will cause the block file to be saved into the file ``filename'' in something that approximates GCG .msf format. Warning! This has not been fully tested.


Sets the colour used for numbering at the top of the alignment (no American spelling at the moment). In this example, colour number 4 has been defined (See the DEFINE_COLOURcommand if you are not sure what this means).

SINGLE_PAGEIf this is set, ALSCRIPT assumes everything will be plotted on one page. At the moment, all this does is write the bounding box for the figure, so encapsulating the PostScript. This may allow the output of alscript to be imported into word processors etc, but probably not all.

ID_ONLY_ON_FIRST_LINEIf this is present, then sequence identifiers will only be printed on the first line of the alignment. Often this looks better for small alignments than the default.


Sets the colour used for the background to the alignment. This can be useful for preparing figures for projection. At the moment this only works reliably when the SINGLE_PAGEis also set.