Garlic Tutorial

Lesson 9 - Venn Diagram

In this simple lesson, you will learn how to prepare the Venn diagram with some residue counts. There is nothing special in this routine and experts will not find it very useful. It is primarily intended for students and other newbies, which are interested in the residue composition of the given protein.

The only information required to prepare the Venn diagram is the protein sequence. In this example, the sequence will be extracted from PDB data. Another approach will be to load the sequence from some FASTA file. The PDB file used here is 1HUC.pdb, but you can replace it with any PDB file which contains the protein structure.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure.

load 1HUC.pdb

Step 3 - discard all hetero atoms:

sel het
sel com

Step 4 - restrict your selection to chains A and B:

res a,b/*/*/*

Step 5 - extract sequence:

seq from 1

Step 6 - draw Venn diagram with residue counts:

venn

Step 7 - discard the structure:

dis all

Step 8 - clear the sequence buffer. You can omit this command.

seq reset