COM. ARGUMENTS APPLIES 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, 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 (balls & sticks)
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 selection Set 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
CRE none main sequence buffer,
main structure buffer
Create new structure
DIS structure_identifier
*, all
structure Discard structure
DOC identifier_1 identifier_2
OFF
Two structures Prepare two structures
for docking
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 given object
NEI none, OFF main window Show or hide seq. neighborhood
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
sequence buffer Plot hydrophobicity and/or
hydrophobic moment
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 selection 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, sequence 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, WHI hydrophobicity scale Choose hydrophobicity scale:
Eisenberg, Kyte-Doolittle, White
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, POL, POS,
SEQ, SID, SMA, SPH, TIN, TM, TRA, TRI
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 the specified 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 Set draw. style for disulf. bonds
STE none, OFF main window Switch to stereo mode
STI radius (angstroms) structure Set stick radius (balls & sticks)
STR = one_letter_code, LOAD filename,
FROM structure_identifier, COPY,
SAVE filename, RESET
sec. struct. buffer,
ref. sec. struct. buffer
Manipulate sec. structure buffer
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, 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