COLOUR_TEXT_REGION x y x1 y1 colour
Sets the colour for TEXT command output. Similar syntax to COLOUR_REGION, FONT_REGIONetc.
COLOUR_LINE_REGION x y x1 y1 colour
Set the colour for LINEs in a region.
CALCONS x y x1 y1
Calculate conservation values according to Zvelebil et al. for the designated region. (See Livingstone &Barton 1993 for details and further refs)
MASK CONSERVATION cutoff
If CONSCAL has been used, then mask residues according to the conservation cutoff.
e.g. MASK CONSERVATION 10 would mask all identities, MASK CONSERVATION 6 would mask reasonably conserved positions. See examples for more on this command.
HELIX x1 y x2
Draw a helix from x1 to x2 of sequence y.
STRAND x1 y x2
Draw a strand from x1 to x2 of sequence y.
COIL x1 y x2
Draw a coil (horizontal line) from x1 to x2 of sequence y.
Set reference numbers to work relative to sequence number <seqnum>. This means that in all subsequent commands, ALSCRIPT will translate your x values into absolute position values in the alignment. This is extremely useful since you can annotate your alignment using your favourite sequences as a reference point. You no longer have to translate every x position into the alignment position.
<startnum> is optional. If present, it specifies what the first residue in the displayed sequence is. For example, you may be showing residues 200-500 of a sequence, so <startnum> would be 200 rather than the default of 1. Warning - this is a very new feature and bounds checking is not fully enabled for it.
You can use RELATIVE_TOseveral times in the command file to annotate different sequences. RELATIVE_TO0 resets to the ``normal'' alignment numbering.