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.

Just below the central residue there will be a small black rectangle with a blue arrow. This arrow shows the approximate direction of the main chain.



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 11 which gives 23 residues in the sequence neighborhood. The actual number of visible residues depends on the size of the main window and on the font size. Default font size is 10x20. If this is too large, use 9x15 or 7x14 - these fonts are still readable, but on small displays more suitable if you want the entire sequence neighborhood to be visible.

RELATED COMMANDS
FONT is used to change the font. For example:

fon 7x14

may be used to choose reasonably small (but readable) font.