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 ... F7 (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 F1, F2, F3, F4, F5, F6, F7 | sequence buffer | Plot average hydrophob., hydrophobic moment, sided hydrophobicity or some other function
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, 2NZ3, 3C4, 3CZ4, 3NZ4, 3C5,
3CZ5, 3NZ5, 4C5, 4CZ5, 4NZ5, 3C6, 3CZ6,
3NZ6, 4C6, 4CZ6, 4NZ6, 5C6, 5CZ6, 5NZ6,
4C7, 4CZ7, 4NZ7, 5C7, 5CZ7, 5NZ7, 5P7,
6P7, 4C9, 4CZ9, 4NZ9, 5C9, 5CZ9, 5NZ9

structure,
selection

Define new selection
(overwrite previous);
C = charged,
Z = zwitterionic,
N = negative,
P = polar

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 and output win. | Change text background
TFG | color_specification | input and 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