A simple users manual for SAE.  Leslie Grate

NEW BUTTONS
GSi, GSs, Si, Ss send display commands to rasmol.  GS means
Guide Sequence, and the i and s mean individual sequence, or
the associated structure string.  GSi displays in rasmol the guide
sequence, GSs displays in rasmol the guide sequence structure string.
Ss and Si do the same thing, but for the first currently selected
sequence.

Editing mode Key Definitions:
'o'  OPEN adds 5 columns to the alignment.
'c'  CLOSE up needless columns left of cursor.
'i'  Changes column to an INSERT type.
'a'  Changes column to an ALIGNMENT type.
SPACE . -     Push characters right.
BACKSPACE ^h  Pull characters left.
'm'  place left edit region mark at cursor.
'M'  place right edit region mark at cursor.
'u'  turn OFF region editing.
'U'  turn ON region editing.
'>'  Push characters right, RESPECTING REGIONS.
'<'  Push characters left, RESPECTING REGIONS.

arrow keys move cursor.

Editing functions.
You have to enter EDITING MODE, via the EDIT button.
(in this mode, you cannot 'select' sequences).
Editing is VERY primitive:
there are 2 'block of characters' movement commands.
The SPACEBAR (or . or -) PUSH the characters to the
right of the cursor.  The BACKSPACE (or ^h) PULLS
the block leftward.
The key 'o' OPENS space (currently 5 columns) in the
alignment.
The 'type' of an alignment column can be changed.  The 'a'
key makes a column an ALIGNMENT column, the 'i' key
makes it INSERT (as normally defined in the SAM sense).
Columns that are not valid in the SAM sense are drawn
in a VIOLET color.
The left mouse button and the arrow keys move the cursor.

You can SAVE (using the 'write file' command) which
tells you how many errors there are before letting
you write the file.

Sae reads multiple numbers of a2m type files.
If special sequence names of DSSP or STRUCTURE
are found, they are put up top, and are assumed to be
structure string information.
All data is assumed to be consistent with a single
alignment, no alignment is done by the program.

Sae can talk to rasmol, and can send it select commands
based on regions in the alignment you select.
The command line switch -R turns off use of rasmol.
Sae uses the environment variable RASMOL as the string
to tell the shell to run rasmol.
A good setting of this variable is in your .cshrc
setenv RASMOL /projects/compbio/bin/$ARCH/rasmol

A second good variable to set is where some PDB files
are:
setenv PDBDIR /projects/compbio/data/pdb

The graphics display of sae is a simple pane with
the multiple alignment.  The RIGHT mouse button brings
up the command menu, the LEFT button 'selects' sequences,
and sweeping with the middle
button (no feedback yet) selects a region.

The 'selected' sequences can be hidden from view.
The most important function of selection is to choose
the 'master', or guide sequence, which SHOULD BE THE SAME
SEQUENCE THAT IS LOADED INTO RASMOL.  

Since Rasmol only shows one PDB file at a time, all
sequence numbers have to be translated into that numbering
system for the selection to have any meaning.  Sae allows
you to choose what sequence should be the basis for computing
this numbering.  It defaults to the first or second sequence,
but you can change it using the by selection and the
'make Selected Guide Seq' command.  It is the sequence
with the red box around it.

One of the commands is 'Select in Rasmol', which sends
the yellow hilighted region to Rasmol to select.
Three more commands 'Hilight Exact|Similar|DisSimilar'
automatically choose and select columns that are pure,
have all the same 'type' (letters, dots, dashes), or
a mix.
These commands are all additive in that the rasmol display
is not cleared of previous selections.
The command 'Clear similar' resets the Rasmol display.

The colored buttons are display flags.  The CYS button
is specifically to color cysteines (T).  When two cysteines
are in a column, they are drawn in PINK, otherwise DARKGREEN
and BROWN are used.
The other buttons only function in KIMMEN mode.  They allow
or disallow sending to rasmol the selects for the respective
color.

There is a primitive command line driven (no graphics) mode.
The switches -d, -e, -s invoke the above mentioned commands
and write the rasmol commands to stdout.  You can use this
to create scripts.

Examples:
run sae interactively with graphics and rasmol (env RASMOL set)
sae -p$PDBDIR/1pht.pdb xxx.a2m

run sae with no rasmol
sae -R xxx.a2m

run with no graphics to create script commands for selecting
disSimilar and exact match columns
sae -d -e xxx.a2m

Same as above, but includes the load command for the given
pdb file
sae -p$PDBDIR/1pht.pdb -d -e xxx.a2m