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+<HEAD>
+<TITLE> More complex effects - Text Lines, and Masks</TITLE>
+</HEAD>
+<BODY><P>
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+<H2><A NAME=SECTION00011200000000000000> More complex effects - Text Lines, and Masks</A></H2>
+<P>
+Text, lines and masking are meant to be used to annotate the multiple
+alignment. The TEXT command allows any piece of text to be located
+anywhere on the alignment. Clearly, however it makes little sense to
+superimpose the text over the alignment though this can be done! Accordingly,
+you must first make a space to put the text in. Usually, this will be a
+few lines below the multiple sequence alignment, but you may want to
+add text at the top, or somewhere in between two sequences. You can make
+space in two ways. Either by editing the block-file to introduce "dummy"
+sequences at the locations you want, or by making use of the ADD_SEQ
+command.
+<P>
+The ADD_SEQ command has two arguments, the sequence after which you want
+further sequences to be added, and how many blank sequences you need.
+Thus, we can reserve space for 5 lines of text underneath a 10 sequence
+multiple alignment with the following command.
+<P>
+ADD_SEQ 10 5
+<P>
+we can then put text below the alignment at the 20th residue.
+<P>
+TEXT 20 13 "Active Site His"
+<P>
+or any other position.
+<P>
+Similarly, we could draw a vertical line to point out which residue we mean
+<P>
+LINE LEFT 20 13 11
+<P>
+And change the font of the text to number 7 (whatever that has been set to):
+<P>
+FONT_RESIDUE 20 13 7
+<P>
+You can have multiple ADD_SEQ commands, but they must occur in sequence order.
+Thus:
+<P>
+<PRE><TT>
+ADD_SEQ 0 5
+ADD_SEQ 5 12</TT></PRE>
+is legal.
+But
+<PRE><TT>
+ADD_SEQ 5 12
+ADD_SEQ 0 5</TT></PRE>
+<P>
+Is NOT!! NO CHECKING IS performed by the program for this error - so beware!
+<P>
+Note that add_seq commands refer to the actual sequence number as
+implied by the block file, not the number after applying the add_seq
+command. Thus, for a four sequence block file, if you want to add
+space for three sequences before sequence 1 and two sequences after
+sequence 3, the commands would be:
+<P>
+<PRE><TT>
+ADD_SEQ 0 3
+ADD_SEQ 3 2</TT></PRE>
+<P>
+Text added with the TEXT command will not be split across page breaks,
+so you may in some circumstances need to fiddle a little with the
+location/pointsize for the text to get the desired result.
+<P>
+Masking is a technique for drawing irregular shaped outlines, or
+shaded regions - this should not be confused with the MASK family of commands
+described below. For example a histogram can be added to the bottom of
+an alignment by first defining some dummy sequences in the block-file
+that have letters building up the shape of the histogram, then using
+the SURROUND_CHARS or SHADE_CHARS commands together with the SUB_CHARS
+command to produce the desired effect. An example of this operation
+being used to show frequencies of secondary structure predictions is
+shown in example1.als and in the Protein Engineering paper.
+<P>
+<HR> <A NAME=tex2html255 HREF=section3_12.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html253 HREF=section3_11.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html249 HREF=subsection3_11_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html257 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
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+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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