Garlic Tutorial

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.


These lessons should help you to learn how to use garlic. Command are given in lowercase, in a short form, but you can use the long form as well as the uppercase letters. File names should be specified in the correct case.


In addition, you should read the pages describing garlic commands and controls !

Lesson 1 - Get familiar with garlic
Lesson 2 - Load a small structure
Lesson 3 - Playing with two structures
Lesson 4 - Drawing styles and color schemes
Lesson 5 - How to select atoms
Lesson 6 - Ramachandran plot
Lesson 7 - Helical wheel plot
Lesson 8 - Plot averaged hydrophobicity and hydrophobic moment
Lesson 9 - Venn diagram
Lesson 10 - Semitransparent plane
Lesson 11 - Create small structure
Lesson 12 - Replace selected residues


The scripts listed below may be used to demonstrate the available drawing styles for atoms and bonds, as well as some predefined color schemes. These scripts were included into the garlic source package 28. March 2000. If you have an older package, copy these scripts to your local host. There are two ways to copy scripts:
(1) Click here to download them via ftp.
(2) Go to the page which contains the script you selected. Mark and copy the script. Paste it into a local file. Recommended file names: 1: atoms.script, 2: bonds.script, 3: colors.script, 4: dance.script .

Script 1 - Drawing styles for atoms
Script 2 - Drawing styles for bonds
Script 3 - Predefined (hard-coded) color schemes
Script 4 - Dancing tryptophan