# NEI, NEIGHBORHOOD

NAME
NEI, NEIGHBORHOOD - hide or show the sequence neighborhood.
SYNOPSIS
NEI
NEI VER
NEI OFF
NEIGHBORHOOD
NEIGHBORHOOD VERBOSE
NEIGHBORHOOD OFF
DESCRIPTION
Hide or show the sequence neighborhood of the residue covered by the pointer. When you cross an atom or bond with the mouse pointer, the output window will contain some useful information about this atom. In addition to this, the top portion of the main window will contain some data about the residues before and after the residue to which this atom belongs. The central 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, execute the command:
nei off
If you want to remove the sequence neighborhood permanently, find this section in the configuration file .garlicrc and use the keyword "no" instead of the previus keyword ("verbose" or "yes"):

# Sequence neighborhood of the residue under the pointer may be hidden, # visible and short or visible and verbose (no/yes/verbose): show sequence neighborhood: verbose

By default, the sequence neighborhood will be visible and verbose.
KEYWORDS
If used without any keyword, the command NEI will make the sequence neighborhood visible and short. The string at the top of the main window will contain only residue names, without serial numbers and chain identifiers. The keyword VER (long form: VERBOSE) may be used to force writing of residue serial numbers and chain identifiers in addition to residue names. The keyword OFF is used to hide the sequence neighborhood.
The keyword VER (VERBOSE) was introduced in version 1.4 of the program. The verbose output was set as default in the configuration file, .garlicrc.
EXAMPLES

COMMAND | DESCRIPTION
nei off | Hide the sequence neighborhood.
nei | Show short sequence neighborhood (residue names, without serial numbers and chain identifiers).
nei ver | Show verbose sequence neighborhood (residue names, serial numbers and chain identifiers).

NOTES
(1) Residues in the sequence neighborhood are listed in direction from amino- to carboxyl-terminal residue.
(2) If the current residue is close to the polypeptide chain end, it will be displaced from the central position.
(3) The half-width of the sequence neighborhood is defined as NEIGH_HALF_WIDTH in defines.h; the total number of residues in the sequence neighborhood is:
2 * NEIGH_HALF_WIDTH + 1.
Default NEIGH_HALF_WIDTH value is 7 which gives 15 residues in the sequence neighborhood. The actual number of visible residues depends on the size of the main window and on the font size.