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 | 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 |