Garlic Commands

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software, Damir Zucic.
The image in the main window is controled by CONTROLS and by COMMANDS. This page contains the list of garlic commands.

Garlic commands are strings, consisting of one or more words. A command is executed when you press the RETURN key (this key is labeled ENTER on some keyboards). Note that ENTER key on the numeric keypad (the one in the bottom right corner of your keyboard) is NOT the right key! Commands will be displayed in the area called the input window.

The input window is placed at the bottom of the main garlic window, left justified. You don't have to the click into this area to enter the command string - just type it. The input window is capable to display a single error message (top) and a single command (bottom).

You can access previously executed commands by using arrow keys on your keyboard (the UP arrow scans the history buffer backwards and DOWN arrow in the opposite direction).

This page contains the alphabetic list of garlic commands with a short description and with link to detailed description.

Commands are generally case insensitive, but file names are case sensitive because unix (linux) is case sensitive.

ADD ADD Expand current selection.
ANG ANGLE Define angle.
ATO ATOMS Change atom drawing style.
BAC BACKBONE Draw backbone.
BAL BALLS Set the ball radius.
BG BACKGROUND Change main window background color.
BLU BLUR Blur (soften) the image in the main window.
BON BONDS Change bond drawing style.
CAT CATCH Catch the specified structure.
CEN CENTER Change the internal coordinate system origin.
COL COLOR Set color.
COM COMPARE Compare two sequences.
CRE CREATE Create structure.
DIS DISCARD Discard structure.
DOC DOCK Prepare two structures for docking.
EDI EDIT Edit structure.
EXE EXECUTE Execute garlic script.
EXI EXIT Quit garlic session.
EXP EXPAND The same as ADD.
FAD FADING Change color fading style or parameter(s).
FG FOREGROUND Change main window foreground color.
FON FONT Change font.
GRO GROUP Group (catch simultaneously) the specified structures.
HID HIDE Hide selected atoms.
HYB HYBONDS Generate hydrogen bonds.
IGN IGNORE Ignore (this command does nothing).
LAB LABELS Show labels.
LOA LOAD Load the specified file.
LOG LOG Write commands to log file.
MEM MEMBRANE Membrane manipulation.
MON MONO Switch to mono mode.
MOV MOVE Define which object should be moved.
NEI NEIGHBORHOOD Show or hide the sequence neighborhood.
PAU PAUSE Pause execution (useful in scripts).
PLA PLANE Plane manipulation.
PLO PLOT Plot averaged hydrophob. and/or hydrophobic moment.
POS POSITION Move structure to specified position.
PRO PROBE Set the bond probe radius (used to draw nice bonds).
QUI QUIT The same as exit.
RAD RADIUS Define sphere radius (used for selection).
RAM RAMACHANDRAN Draw Ramachandran plot.
REA READ The same as LOAD.
REF REFRESH Switch graphics refreshing on or off.
REG REGISTER Register garlic.
REP REPLACE Replace selected residues.
RES RESTRICT Restrict current selection.
ROT ROTATE Rotate structure.
SAV SAVE Save atomic data to file.
SCA SCALE Select hydrophobicity scale.
SEL SELECT Select atoms.
SEQ SEQUENCE Sequence buffer manipulation.
SET SET Set the specified dihedral angle.
SHO SHOW Show selected atoms.
SLA SLAB Change slab style or parameter(s).
SSB SSB Change drawing style for disulfide bonds.
STE STEREO Switch to stereo mode.
STI STICKS Set the stick radius.
STR STRUCTURE Secondary structure manipulation.
TAG TAG Assign tag (short text) to structure.
TAK TAKE The same as CATCH.
TBG TEXT_BACKGROUND Change text background color.
TFG TEXT_FOREGROUND Check text foreground color.
TIT TITLE Add title to the main window.
TRA TRANSLATE Translate structure.
VEN VENN Draw Venn diagram.
WHE WHEEL Draw helical wheel.
WIN WINDOW Set sliding window width.