| 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 | 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 |