COM. ARGUMENTS APPLIES TO DESCRIPTION
ADD the same as for SEL selection Add to selection
ANG angle (degrees) helical wheel,
hydrophob. mom.
Angle for helical wheel
and hydrophobic moment
calculation
ATO 0, 1, 2, 3, 4, 5, 6, 7, BAL, BA2, SMA, SM2,
COV, CO2, SPA, SP2, BIG, BI2
selection Set drawing style for atoms
BAC 0, 1, 2, 3, 4, 5, OFF selection Draw backbone
BAL radius (angstroms) structure Set ball radius
BG color_specification main window Change background color
BLU width height, OFF main window Blur (soften) image
BON 0, 1, 2, 3, 4, 5, NICE,
REFRESH
selection Set bond style or
refresh (reset) 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, cold (default),
hot, monochrome, cpk, size, zebra,
chain, hyphob, weighted
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
CRE none main seq. buffer,
main struct. buffer
Create new structure
DIS structure_identifier
*, all
structure Discard structure
DOC identifier_1 identifier_2
OFF
Two structures Prepare two structures
for docking
DUM AVE filename,
HYD filename,
F1 ... F5 (with filename)
Hydrophobicity functions Dump numeric values for
selected hydrophob. f.
EDI OFF, ATO, BON atom1 atom2, CLI,
DIM, MAI, OME, PHI, PSI, SID
structure Edit structure
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
GRO id1 id2 ... idN,
ALL, SAV filename, SSC filename
structure(s) Group structures
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
MEM none, OFF, BET, RAD radius,
THI thickness, TRA transparency
membrane Show or hide membrane,
set properties
MON none main window Switch to mono mode
MOV ALL, MEM, PLA, STR struct., memb., plane Attach controls to object
NEI none, VER, OFF main window Show or hide
sequence neighborhood
PAT = res_name_list1 / * / res_name_list2 ...
TOL number_allowed_errors
pattern buffer define sequence pattern
or set pattern tolerance
PAU none garlic script Pause script execution
PLA none, OFF, RAD radius,
TRA transparency
plane Show or hide plane,
set properties
PLO HYD, MOM, OFF,
HYD start_residue end_residue,
MOM_start_residue end_residue
SID start_residue end_residue
sequence buffer Plot average hydrophob.,
hydrophobic moment
or sided hydrophob.
POS x, y, z structure Move to (x, y, z)
PRO radius (angstroms) structure Set probe radius
QUI none garlic session Quit garlic session
RAD radius (angstroms) Selection sphere Change sel. sphere radius
RAM none, SEL, OFF structure Draw Ramachandran plot
REF none, OFF main window Refreshing on/off
REG none mail Register garlic
REP none structure, seq. buffer Replace selected residues
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, INT, IN2, OCT, DIF hydrophobicity scale Choose hydrophob. scale:
Eisenberg, Kyte-Doolittle,
interface, octanol
SEL chains/res_nums/res_names/atom_names,
residue_numbers,
residue_names,
*, ALL, ABO, ACI, ALI, ALT, BAD,
BAS, BEL, CHA, CIS, COM, HET, PHO,
MAI, MOD model_number, NEG, PAT,
POL, POS, SEQ, SID, SMA, SPH, TIN,
TM, TRA, TRI, 2C3, 2CZ3, 3C4, 3CZ4,
3C5, 3CZ5, 4C5, 4CZ5, 3C6, 3CZ6,
4C6, 4CZ6, 5C6, 5CZ6, 4C7, 4CZ7,
5C7, 5CZ7, 5C9, 5CZ9, 5P7, 6P7
structure,
selection
Define new selection
(overwrite previous)
SEQ = three_letters_code, LOAD filename,
FROM structure_identifier, COPY,
SAVE filename, SWN filename, RESET
sequence buffer,
reference seq. buffer
Manipulate sequence
buffer
SET PHI, PSI, OME, CHI1, CHI2, CHI3,
CHI4, CHI5 (angle required, degrees)
structure Set dihedral angle
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, NICE disulfide bonds Style for disulf. bonds
STE none, OFF main window Switch to stereo mode
STI radius (angstroms) structure Set stick radius
STR = one_letter_code, LOAD filename,
FROM structure_identifier, COPY,
SAVE filename, RESET
sec. struct. buffer,
ref. sec. struct. buffer
Manipulate secondary
structure buffer
TAG "string", OFF structure Assign or remove tag
TBG color_specification input&output win. Change text background
TFG color_specification input&output win. 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, CLOCKWISE,
start_index end_index,
start_index end_index CLOCKWISE
sequence buffer Draw helical wheel
WIN number_of_residues sliding window Set sliding window width