BIOLOGY 3521-- BIOCHEMISTRY
Fordham University -- Spring 1999 
Computer Use and Molecular Graphics
Walsh Library Electronic Information Center
2/10/99
Mac Info Upate
 E-mail Update
Crash Warning on PCs with MAGE
 
 
Main Selections:
1. General Computer Information for Walsh Library Electronic Information Center
2. Molecular Graphics for Protein and Nucleic Acid Structures
General Computer Information for Walsh Library Electronic Information Center (EIC)
Computer Labs A and B in the Walsh Library Electronic Information Center (EIC)
  • Computer Labs A and B are in the basement of Walsh Library in the Electronic Information Center. Computers in these labs have access to the internet, high speed printers, and are configured for using the molecular graphics in Biochemistry.
    • Lab A is a Macintosh Lab
    • Lab B is a PC Lab
  • These labs may have scheduled classes in them. You must use the labs only when scheduled sessions are not in the labs. Ask at the EIC desk to determine if the labs are open.
  • Note that other computers in the EIC may not have internet access and they do not have the molecular graphics programs for Biochemistry.
Using the computers in Walsh EIC Computer Labs A and B

Macintosh (Lab A)

PC (Lab B)

Printing Lecture Notes, Printing Problems, and Lecture Updates

Printing

Print the notes using a two page layout at 90% to save paper (see the notes and handouts from the first day of class)

For the Macintoshes
  • Under the file menu, select Page Setup
  • Select 2 UP for the page layout toggle window
  • Click OK to save the changes
  • Print as usual

For the PCs

  • When you select print from Netscape
    • Choose properties in the window
    • Select 2 pages/sheet
    • Print as usual
Check to see that all the material on the pages has printed.
Make sure the entire page has loaded in the WWW browser prior to printing.
Be sure that the printout contains any embedded graphics and no text is lost.
Note that with multiple users printing from the printers, the printers may be slow in printing your material.
If you are having trouble printing, go to the EIC desk to get help.
If they do not provide help or resolve your problem, please bring the problem to my attention.
Lecture Updates
Please note the year and last date of the lecture update
  • For subsequent lecture, 1998 lectures are currently on the server
  • These lectures are updated as we go through the course.
  • Always check before you print the notes that a 1999 version of the lecture is on the server
    • If the date at the top of the lecture says 1998 and the Version date is 1998 the notes are clearly from last year. You may print them to get an overview of what I will talk about, but note that I update and modify the notes .
  • In general, I will attempt to have the updated 1999 version notes I use in class available on the server late afternoon or the night before the lecture.
    • Always check the date of the lecture I am using in class to be sure you have the most recent version.
    • In some cases several lectures are updated just prior to their use if I find errors.
 
In unusual circumstances where there are serious printing problems, I will place three copies of the lecture notes for the class (in many cases with the figures) on reserve at the Science Library Desk in Walsh. The notes will be placed on reserve after class. Course homework problems and study aids will also be placed on reserve.
 
 
Sending e-mail to me from the Walsh Labs
There are currently two options for sending e-mail:
Netscape Browser
Telnet
I recommend you use the Netscape Browser method (if you are using your Fordham e-mail account)
  • Enter the material and hit return or select the OK
  • You should now have access to your mail and be able to send mail
 
Problems with Graphics or Molecular Visualization
  • If you are trying to view an exam or exam key (perhaps other things as well) and nothing loads within the browser window, the problem is with Adobe Acrobat Reader 3.01 and the PDF viewer plug-in
Kinemage and Mage graphics: Kinemages and Launching the MAGE 4.2 application
PCs
  • BEWARE OR YOU WILL CAUSE A CRASH - READ BELOW
    • Downloading and viewing a second kinemage file
      • For reasons that are currently not clear, before you select another link in the notes to download an additional kinemage file (this means you already have the program open and have viewed a kinemage), you must first QUIT MAGE before you select the link on the computer will crash and lock.YOU MUST QUIT THE MAGE PROGRAM FIRST BEFORE YOU SELECT THE LINK IN THE NOTES TO SEE ANOTHER FILE
    • IF YOU DON'T QUIT MAGE BEFORE YOU DOWNLOAD ANOTHER KINEMAGE THE COMPUTER WILL CRASH
  • If you select a link that initiates downloading a kinemage file to be launched with Mage, the Mage program should automatically launch and be the front window with the kinemage illustration
  • Note that sometimes the Mage window will be behind the Netscape window and you will have to bring that window to the froNT
  • If theto save with a suffix .kin the Mage Program should launch and Netscape asks you to pick an application
    • Go C:\
    • Select the Biochemistry directory
    • Select MAGE 4.2 as the application
  • This should launch the downloaded kinemage file with the application MAGE as a separate window
  • Close the window or exit the application before you download another kinemage for viewing or the computer will freeze
 
Macintoshes
  • When a kinemage is selected via a hypertext link, the file should download and be opened with the MAGE program as observed in class.
  • Problems with this may not be solvable at your level due to the configuration imposed on the Macs and their poor management

Molecular Graphics for Protein and Nucleic Acid Structures

Selections:

Programs for Structure Visualization -- Structures of molecules can be presented in 3-dimensionally for better visualization. These presentations require particular software to visualize the files. Several types of software have been configured as applications or helpers for the Netscape WWW browser in the Walsh Computer Labs A and B. These include
Chemscape Chime (a Netscape helper application)
RasMol (an application which has been integrated into Chemscape Chime
MAGE software and Kinemages (this application can also be configured as a Netscape helper)
Network Entrez and C3nD
For general information on the Chemscape Chime, Kinemage/Mage, and other graphics programs
used for these lectures and a listing of many of the files used in the lectures
see Graphical Presentation of Protein Stuctures
see ProTeach for instructions on using MAGE and instructional kinemages
in the Walsh Library computing labs 
Recommended Tutorials or graphics for Biochemistry 3521
Amino Acids, Peptides, and Protein Structure
 
Visit the Amino Acid ajnd Peptide Structure Tutorial at Carnegie Mellon

Amino Acid Information at Indiana University (Static and Rotatable Images)

Visit the Protein Architecture Tutorial for ProtG at Carnegie Mellon

  • Note that you need the MIME plug-in called Chime for your browser for this to work
  • Study Aid: Quiz on Protein Architecture based on the Protein Architecture Tutorial at Carnegie Mellon

Introductory Biology Version of the Protein Structure Tutorial at Carnegie Mellon (Requires Chime)

Visit the Lysozyme-Substrate Complex at Carnegie Mellon (Requires Chime)

Visit the Hemoglobin Tutorial at Carnegie Mellon (Requires Chime)

Visit the Protein Structure Tutorial at Amherst (Requires Chime)

Protein Structure and Hemoglobin at UMass

Visit the Antibody Tutorial at UMass (Chime Required)

Visit the MHC (Major Histocompatibility Complex) Tutorial at UMass (Chime Required)

 
Instructional files and programs for learning aspects of protein structure are available on both the Macintosh and PC computers in Walsh Library Conputer Labs A and B
  • For information on the ProTeach Files, Kinemages, and MAGE software follow the ProTeach Link
  • Files used in lecture for graphic presentation have links embedded in the lecture notes
    • For a summary of some of the structures presented in class as a separate file and a description of file formats and structure presentations -- see Graphic Presentation
Common Molecules in Biochemistry and Energy Metabolism 
Visit the Molecules in Modern Biology Gallery at Carnegie Mellon

Visit Glycolysis. Chime-generated intermediates on the glycolytic pathway. At Carnegie Mellon (Chime Required)

Visit TCA cycle. Chime-generated intermediates in the tricarboxylic acid cycle. At Carnegie Mellon (Chime Required)

Molecular Biology
Visit the DNA Structure Tutorial at UMass (Chime Required)
 
Visit the Overview of DNA & RNA Structure at Carnegie Mellon (Chime Required)

Visit the Overview of A Tour of tRNA Structure: at Carnegie Mellon (Chime Requried)

Visit the Overview of Structures for Molecular Biology at Carnegie Mellon (Chime Required)

  • Introduction and links to these molecular models:
    • B-Form DNA helix
    • A-Form RNA helix
    • cAMP Receptor Protein (CRP)
    • Human hnRNP A1
    • snRNP U1A
    • EF-Tu, tRNAPhe, and GTP
    • Zif268 zinc finger

Other tutorials at Carnegie Mellon (Chime Required)

Structural and other Databases for Proteins and Nucleic Acids

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