Assignment #1 - System Configuration and Email

**************************** Assignment 1 *************************************
Course: Chemistry 125   //  Instructor: Max Kopelevich 
Due Date: Wed, October 1, 2008
Notes: submit assignment by e-mail to instructor
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1. Describe one of the computer systems that you've been using at home, school,
or work. Provide some details about the make/model of the computer, memory,
disk space (total/free), printer, and any other attached peripherals.

2. Find out what Operating System is installed on your system (name and
version number).  Do you update the OS regularly?  Do you have antivirus
software installed?

3. Does this computer have network connectivity (cable, DSL, wireless,
LAN)?  (Optional) Find out the computer's IP address, gateway, and netmask.

4. What are some of the applications that you most often use on your computer?

5. What would you like to learn in this class?

**************************** Assignment 1 *************************************

Assignment #1.1 - From Transistors to Microprocessors

• Visit the online Computer History Museum.
• Read Howstuffworks.com pages on PC, Bits and Bytes, Boolean Logic, Microprocessor.

(Optonal) For more detailed information take a look at Wikipedia pages:

• Transistor, Digital_circuit, Integrated_circuit , and Logic gates
• Binary numeral system
• Microprocessor and Random_access_memory
• Computer Storage
• Moore's Law

Assignment #1.2 Reading - Operating Systems

• Data Representation Methods
• Unicode
• Booting
• Operating System
• Microsoft Windows
• Linux
• MacOS
• List of file formats

Assignment #2.1 Reading - Computer Networking

• Computer Networking and Internetworking
• Internet Protocol suite
• Internet

Assignment #3.1 Reading - Internet, WWW

• World Wide Web (WWW or Web)
• Uniform Resource Locator (URL)
• Hypertext Transfer Protocol (HTTP)
• Hypertext Markup Language (HTML)
• Secure Shell (SSH)

Assignment #3.2 - Simple Web Page

• Put together a simple web page.
• On your web page add links to three Chemistry related Sites that you find interesting. Provide a brief description of the Sites.
• Use tutorials at www.w3schools.com to teach yourself HTML, CSS, and JavaScript.

Assignment #5 - PDB and Rasmol/Jmol

1. Take a look at Molecular Models site, here you can pick up coordinate files for many small molecules.
2. Learn about Protein Data Bank (PDB) and retrieve the coordinates of Diphtheria Toxin (refined structure of Dimeric Form) . E-mail the 4 character ID code for the entry to mik@chem.ucla.edu.

3. Use RASMOL on your PC or MAC to view the 3-D structure of Diphtheria Toxin. If you don't have RASMOL download a copy of the program for MAC or Windows or use c125 server and Jmol.

4. To look at some of the advanced capabilities of Rasmol enter the following commands in the command window.

   Set the backbone thickness to 0.5 A thick ( 500 is 2.0 A) with the command

    backbone 100 (in new versions use - backbone 0.5)
   

   Sometimes changing the background to white makes the visualization easier.

    background white
   

   Click on different regions to get the numbering of the chains. Once you have the numbering of all the chains , paint each domain or subdomain in a different color.

    select 1-50
    colour backbone yellow
    select 51-120
    colour backbone blue
   

5. Transfer the pdb file to your c125 class web folder.
6. Use Jmol to include the structure on your web page together with a few lines of background information.

Assignment #6 - Molecular Modeling