2 <TITLE> New Step 2 Commands</TITLE>
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10 <H2><A NAME=SECTION00010200000000000000> New Step 2 Commands</A></H2>
12 COLOUR_TEXT_REGION x y x1 y1 colour
14 Sets the colour for TEXT command output. Similar syntax to COLOUR_REGION, FONT_REGIONetc.
16 COLOUR_LINE_REGION x y x1 y1 colour
18 Set the colour for LINEs in a region.
22 Calculate conservation values according to Zvelebil <em>et al.</em> for the designated
23 region. (See Livingstone &Barton 1993 for details and further refs)
25 MASK CONSERVATION cutoff
27 If CONSCAL has been used, then mask residues according to the conservation cutoff.
29 e.g. MASK CONSERVATION 10 would mask all identities, MASK CONSERVATION 6 would
30 mask reasonably conserved positions. See examples for more on this command.
34 Draw a helix from x1 to x2 of sequence y.
38 Draw a strand from x1 to x2 of sequence y.
42 Draw a coil (horizontal line) from x1 to x2 of sequence y.
44 RELATIVE_TO<seqnum> <startnum>
46 Set reference numbers to work relative to sequence number <seqnum>. This
47 means that in all subsequent commands, ALSCRIPT will translate your x
48 values into absolute position values in the alignment. This is <em>extremely</em> useful since you can annotate your alignment using your
49 favourite sequences as a reference point. You no longer have to
50 translate every x position into the alignment position.
52 <startnum> is optional. If present, it specifies what the first
53 residue in the displayed sequence is. For example, you may be showing
54 residues 200-500 of a sequence, so <startnum> would be 200 rather than
55 the default of 1. <em>Warning - this is a very new feature and
56 bounds checking is not fully enabled for it</em>.
58 You can use RELATIVE_TOseveral times in the command file to annotate
59 different sequences. RELATIVE_TO0 resets to the ``normal''