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):
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.
Step 4 - draw backbone, to simplify the picture:
Step 5 - use different colors for different chains:
Step 6 - select chain A, draw balls and sticks and change color scheme to CPK:
Step 7 - redefine the internal system origin (the rotation center) and
move chain A to the screen center:
pos 0 0 0
Step 8 - restrict the selection to aliphatic amino acids and change color
to yellow (chain A):
Step 9 - select all, make it visible, show only backbone but reduce
the backbone thickness:
Step 10 - hide side chains:
Step 10 - select cysteine residues, but only for chains A and C;
make them visible, use spacefill style:
Step 11 - discard loaded structure: