BME 401: Introduction to Biotechnology

Lab Experiment 1
Introduction to Pymol
Prepared By:
Dr. Hadeel Al obeedallah

Edited by: Dr. Rabah Al abdi

Objectives
1. Download Pymol software

2. Explore the graphical user interface of Pymol software

3. Learn how to access and download Protein Data Base PDB

Introduction
PyMOL is an Open Source molecular viewing engine, rendering tool, and editor that can visualize 3D molecular structure
down to the atomic level, including the X-ray crystallographic structure of proteins, DNA, RNA, carbohydrates,
metabolites, sugars, and much more.

In this lab, you are going to be introduced to Pymol software and how to download Protein Database (PDB) files.

Procedure
1 Exercise 1: download Pymol
1. Go to Pymol website : https://pymol.org/2/
2. Click on “Download Now”
3. scroll down and click on “Buy Licence” under new users, This will take you to the following Page
https://pymol.org/2/buy.html?q=buy
4. Scroll down the page and click on Student/Teacher
5. This will take you to “Registration For Educational-Use-Only PyMOL Builds”, this page will have a
form that needs to be filled by you, please note the following while completing the form :
 Select the “student’’ option
 Include correct information regarding your email address as this is how you will be contacted with
the credentials to download Pymol software.

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  For the “subject matter” you can write “introduction to Biotechnology”

6. After completing the form click on “continue”, this will take you to the agreement page where you
need to accept the terms and conditions and submit the form after that.
7. A “Thank you message for registration” will appear on the screen and you should be contacted by
email shortly, after submission, with the credentials to download the Pymol software.
8. You will receive to your nominated email address an email from [email protected], with the
email title as: PyMOL Educational Use Declaration for … (your name) …
9. The email will have the download agreement
10. scroll down the email page and you will find the following information at the end of the email:

DOWNLOAD URL: ...................

USERNAME: ……………..

PASSWORD: …………………..

11. Follow the link available at (DOWNLOAD URL) and use the user name and the password provided
to complete the installation.

12. remember to activate the license file attached with the Pymol downloads so you get a longer-term
license. Skipping the step of activating the “license file” will lead that you download a Pymol version
that will run only for 30days.

2 Exercise 2: Getting Started with Pymol

Launching the software

 Windows: Click on the Start menu, follow it to Programs (or All Programs on Windows XP), and
then release the mouse on PyMOL.
 On Mac OSX (native version) Double−click on the PyMOL icon in the Applications folder on your
main hard drive

PyMOL's Windows

PyMOL normally starts with two windows: The Viewer Window and the External (Tcl/Tk) GUI Window.

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GUI is an abbreviation for Graphical User Interface, which usually consists of menus, buttons, text boxes,
and other familiar gadgets. By default, PyMOL actually has two GUI's: (1) an "Internal" GUI which appears
inside the Viewer Window, and (2) an "External" GUI which appears inside of its own window. Both GUI's
will eventually be unified into a single interface in the future.

The Viewer Window

The PyMOL Viewer represents the heart of the PyMOL system. This is a single Open GL window where
all 3D graphics are displayed and where all direct user interaction with 3D models takes place.

PyMOL Viewer window with Internal GUI enabled (Default).

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The Internal GUI contained within this window (right) allows you to perform actions on specific objects
and specific atom selections. From top to bottom, it contains an object list, a mouse button configuration
matrix, a frame indicator, and a set of "VCR"−like controls for working with movies.

The Viewer also contains a command line (bottom) which can be used to enter PyMOL commands. It is
also possible to view PyMOL text output in the Viewer window. you can hit the ESC key anytime to
toggle between text and graphics mode inside the Viewer window.

The PyMOL Viewer can be run all by itself, and it provides the complete capability of the PyMOL core
system. If desired, the Command line and Internal GUI can be disabled. Many tasks can be made easier and
more efficient through use of standard menus and controls. For the most part, such gadgets are currently
found in an External GUI window.

The External GUI Window

The default Tcl/Tk External GUI included with PyMOL.

By default, PyMOL comes with a single external GUI window which provides a standard menu bar, an
output region, a command input field, and a series of buttons. One important advantage of the external GUI
window is that standard "cut and paste" functions for text will only work within the External GUI,
and not within in the PyMOL Viewer. Furthermore, you must use Ctrl−X, Ctrl−C, and Ctrl−V to cut,
copy, and paste because a standard Edit menu has not yet been implemented.

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PyMol - Exercise B: Download a PDB from the repository

The PDB archive is a repository of atomic coordinates and other information describing proteins and
other important biological macromolecules. Structural biologists use methods such as X-ray
crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each
atom relative to each other in the molecule. They then deposit this information, which is then
annotated and publicly released into the archive by the wwPDB.

Structures are available for many of the proteins and nucleic acids involved in the central processes
of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets,
and even whole viruses. However, it can be a challenge to find the information that you need, since
the PDB archives so many different structures. You will often find multiple structures for a given
molecule, or partial structures, or structures that have been modified or inactivated from their native
form.

Reminder: Structures have a PDB ID code made of 4 letters and numbers.

1) Open a web browser such as Safari or Firefox.

2) Point your web browser to www.rcsb.org

3) In the Search box enter the protein ID, or just simply insert the name of the molecule and click
SEARCH button

4) A list of various conformations of the searched molecule will come up as well as with all the
information related to each structure. You can download the file of each structure and save it on your
computer.

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Exercise C: (To be completed and submitted before our next Lab)

 download the PDB files of: insulin, DNA Polymerase and Helicase.
 Build the 3D models of : insulin, DNA Polymerase and Helicase using Pymol graphical
interface