COM.	ARGUMENTS	APPL. TO	DESCRIPTION
ADD	the same as for SEL	structure	Add to selection
ANG	angle (degrees)	helical wheel, hydrophobic moment	Angle for helical wheel and hydrophobic moment calculation
ATO	0, 1, 2, 3, 4, 5, 6, 7, BAL, BIG, SPA	selection	Drawing style for atoms
BAC	0, 1, 2, 3, 4, 5, OFF	selection	Draw backbone
BG	color_specification	main window	Change background color
BON	0, 1, 2, 3, 4, 5	selection	Drawing style for bonds
CAT	structure_identifier	structure	Catch structure
CEN	none	structure, selection	Redefine system origin
COL	detailed_color_specification, red, green, blue, yellow, cyan, magenta, white, yellow-green, cyan-green, cyan-blue, magenta-blue, magenta-red, orange, hot, cold, monochrome, cpk, zebra, chain, hyphob	selection	Assign color; do not abbreviate color scheme name!
COM	none, OFF, minimal_score segment_width, CORNER serial1 serial2, ZOOM zoom_factor	both sequence buffers	Compare two sequences
DIS	structure_identifier *, all	structure	Discard structure
DOC	identifier_1 identifier_2 OFF	Two structures	Prepare two structures for docking
EXE	file_name	script file	Execute script
EXI	none	garlic session	Quit garlic session
FAD	FRO shift, BAC shift, OFF, PLA, SPH, CYL, HALF-SPH, HALF-CYL	structure	Change color fading
FG	color_specification	main window	Change text color
FON	font_name	all windows	Change font
HID	none	selection	Hide atoms and bonds
HYB	none, OFF	structure	Generate hydrogen bonds
LAB	none, OFF	selection	Show labels
LOA	file_name	structure_file	Load structure (file)
LOG	file_name, OFF	commands	Log garlic commands
MON	none	main window	Switch to mono mode
MOV	PLANE, STRUCTURE, ALL	structure and plane	Attach controls to struct. or plane
NEI	none, OFF	main window	Show or hide seq. neighborhood
PAU	none	garlic script	Pause script execution
PLA	none, RADIUS, TRANSPARENCY, OFF	plane	Show or hide plane, set properties
PLO	HYD, MOM, OFF, HYD start_residue end_residue, MOM_start_residue end_residue	sequence buffer	Plot hydrophobicity or hyd. moment
POS	x, y, z	structure	Move to (x, y, z)
QUI	none	garlic session	Quit garlic session
RAD	radius (angstroms)	Selection sphere	Change selection sphere radius
RAM	none, SEL, OFF	structure	Draw Ramachandran plot
REG	none	mail	Register garlic
RES	the same as for SEL	selection	Restrict selection
ROT	axis angle (degrees)	structure	Rotate
SAV	file_name file_name SEL	structure, selection	Save atomic data to file (SEL = selection only)
SCA	EIS, KD, WHI	hydrophobicity scale	Choose hydrophobicity scale: Eisenberg, Kyte-Doolittle, White
SEL	chains/res_nums/res_names/atom_names residue_numbers residue_names *, all, aci, bas, cha, com, het, pho, mai, neg, pol, pos, sid, sma, tin	structure, selection	Define new selection (overwrite previous)
SEQ	= three_letters_code, LOAD, FROM, COPY, SAVE, SWN, RESET	sequence buffer, reference seq. buffer	Manipulate sequence buffer
SHO	none	selection	Show atoms and bonds
SLA	FRO shift, BAC shift, OFF, PLA, SPH, CYL, HALF-SPH, HALF-CYL	structure	Change slab
SSB	0, 1, 2, 3, 4, 5	disulfide bonds	Drawing style for disulfide bonds
STE	none, OFF	main window	Switch to stereo mode
TAG	"string" OFF	structure	Assign or remove tag
TBG	color_specification	input&output window	Change text background
TFG	color_specification	input&output window	Change text color
TIT	identifier x y "string" identifier x y identifier OFF	main window	Add, move or remove title
TRA	axis shift	structure	Translate
VEN	none, OFF, start_residue end_residue	sequence buffer	Draw Venn diagram with statistics
WHE	none, OFF, start_residue end_residue	sequence buffer	Draw helical wheel
WIN	number_of_residues	sliding window	Set sliding window width