Lesson 7

# Garlic Tutorial

## Lesson 7 - Draw Helical Wheel

In this lesson, you will learn how to prepare the helical wheel plot. This plot may be used to identify amphipatic segments in a protein sequence, i.e. the amphipatic helices. In this lesson, the solved structure will be used for demonstration. For more details, read this (WHEEL command description).
You can use any protein structure for this lesson. In this example 1HUC.pdb is used, though you can use any protein structure.
Step 1 - start garlic (if not started already):
garlic
Step 2 - load the structure. You should have your PDB file (here 1HUC.pdb) somewhere in the search path (if you defined the environment variable MOL_PATH), or in your current working directory.
loa 1HUC.pdb
Step 3 - select all atoms except hetero atoms. If this is not done the hetero "residues" (i.e., solvent molecules) will corrupt the helical wheel plot. The trick is to select hetero residues, and then to select complement. You don't have to hide hetero residues, so you can skip the command hide.
sel het
hide
sel com
Step 4 - check the number of chains in human cathepsin B. If there are two or more chains, the residue serial number should not be used as unique residue identifier.
color chain
Step 5 - there are obviously four chains. Hide all chains except B. Hide everything, after that select only the chain B and make it visible. Hetero residues will not be included into selection, so the step 3 was in fact unnecessary.
sel all
hide
sel b/*/*/*
show
Step 6 - try to find one helix at the chain B surface. Helices may be easily recognized if using backbone representation of the protein. It is also practical to use the geometric center of the chain B as the rotation center, and to move it to the screen center.
bac
cen
pos 0 0 0
Step 7 - play with the chain B to find this helix:

76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86
PRO | ALA | GLU | ALA | TRP | ASN | PHE | TRP | THR | ARG | LYS

Step 8 - copy the sequence of the chain B to the main sequence buffer. Note that the helical wheel plot uses the sequence which is stored in the main sequence buffer. Right now this buffer is empty!
seq from 1
Step 9 - draw helical wheel for residues from 76 to 86:
wheel 76-86
Step 10 - return to the main drawing mode. Hit the escape key or type the following command:
whe off
Step 11 - discard loaded structure:
dis all
Step 12 - clear the main sequence buffer:
seq reset

Do not forget that for helical wheel plot, the main sequence buffer should be initialized!