Garlic Tutorial

Lesson 5 - How to Select Atoms

In this lesson, you will learn how to select atoms. The command select (or whatever command plays this role) is one of the most important commands in every molecular visualization program.

For this lesson, you will need a true protein structure, not just a single amino acid as in previous lessons.

Step 1 - obtain the protein structure:

Use you web browser to access The Protein Data Bank (www.rcsb.org) .
Type 1HUC into the small search field. Start the search and wait for the answer.
Choose the option "Download/Display File".
Finally, choose file format "PDB", compression "none" in the section "Download the Structure File" and wait.

Step 2 - start garlic (if necessary):

garlic

Step 3 - load the structure. You should have the file 1HUC.pdb somewhere in the path searched by garlic (if you defined the environment variable MOL_PATH), or in your current working directory.

loa 1HUC.pdb

Step 4 - draw backbone, to simplify the picture:

bac

Step 5 - use different colors for different chains:

col chain

Step 6 - select chain A, draw balls and sticks and change color scheme to CPK:

sel a/*/*/*
bac off
bon 4
ato bal
col cpk

Step 7 - redefine the internal system origin (the rotation center) and move chain A to the screen center:

cen
pos 0 0 0

Step 8 - restrict the selection to aliphatic amino acids and change color to yellow (chain A):

res ali
col yellow

Step 9 - select all, make it visible, show only backbone but reduce the backbone thickness:

sel *
sho
bac 3

Step 10 - hide side chains:

Step 10 - select cysteine residues, but only for chains A and C; make them visible, use spacefill style:

sel a,c/*/cys/*
show
ato spa

Step 11 - discard loaded structure:

dis all