NAME
NEI, NEIGHBORHOOD - hide or show the sequence neighborhood.
SYNOPSIS
NEI
NEI OFF
NEIGHBORHOOD
NEIGHBORHOOD OFF
DESCRIPTION
Hide or show the sequence neighborhood of the current residue. The current
residue is the residue to which the atom covered by the mouse pointer belongs.
When you cross an atom or bond with the mouse pointer, the output window
will contain some useful information about this atom. The top portion of
the main window will contain the list of the residues around this atom.
The central residue (called also "the current residue") will be enclosed in
a small rectangle. The entire sequence neighborhood will be enclosed in a
wide rectangle.
If you are not interested in the sequence neighborhood of the current residue,
execute the command:
nei off
If you want to remove the sequence neighborhood permanently, find this section
in the configuration file .garlicrc and replace the keyword "yes" by "no":
# Sequence neighborhood of the residue under
# the pointer may be visible or hidden (yes/no):
show sequence neighborhood: yes
By default, the sequence neighborhood will be visible.
KEYWORDS
The only keyword is OFF. If used without any keyword, the command NEI will
make the sequence neighborhood visible. If combined with the keyword OFF,
the command will hide the sequence neighborhood.
EXAMPLES
COMMAND
DESCRIPTION
nei off
Hide the sequence neighborhood.
nei
Show the sequence neighborhood.
NOTES
(1) Residues in the sequence neighborhood are listed in direction from amino-
to carboxyl-terminal residue, left to right.
(2) If the current residue is close to polypeptide chain end, it will be
displaced from the central position.
(3) The output window is visible in the bottom right corner of the main window.
