Lesson 3

# Garlic Tutorial

## Lesson 3 - Playing with Two Structures

In this lesson, you will learn how to work with two or more structures. The original source package contains two PDB files: trp.pdb and phe.pdb. Each contains a single amino acid: trp.pdb = tryptophan, phe.pdb = phenylalanine. In this lesson, tryptophan will be colored blue, while phenylalanine will be colored red. Note the role of the command cat (catch).
Step 1 - start garlic (if necessary):
garlic
Step 2 - load trypthophan:
loa trp.pdb
Step 3 - change TRP color to blue:
col blue
Step 4 - load phenylalanine:
loa phe.pdb
Step 5 - change PHE color to red:
col red
Two structures will be distinguished by color and by the identifier: tryptophan is treated as structure number 1, and phenylalanine is treated as structure number 2. Two structures are now overlapping.
Step 6 - move tryptophan to the left:
cat 1
pos -5 0 0
Step 7 - move phenylalanine to the right:
cat 2
pos 5 0 0
Step 8 etc. - use the command cat (catch) to rotate structures one by one:
Use cat 1 and cat 2 to catch and rotate structures, one by one.
Translate both structures to the position where they will be overlapped, but do not use keyword pos!
When finished, discard loaded structures:
dis all