Biochemistry Online: An Approach Based on Chemical Logic
Jmol Files
02/06/2013
The following information about the safe use of Java with Jmol comes from Proteopedia.
Jmol require Java. Jmol can be used, in any web page containing it, to report the version of Java currently installed: Click on Jmol, then on About Jmol. There are several free websites that report your java version, such as Java Tester. Java.Com also reports the java version on Windows: click on Do I Have Java?. Java has historically had flaws enabling criminals/vandals to commit identity theft and to compromise computers. Simply visiting a malicious website with a java-enabled web browser can compromise your computer.
How can you minimize your risk? Whenever an update for Java is available, install it. To confirm that you have the latest Java, visit java.com, click on the link "Do I have Java?" and then on the button "Verify Java". Do not visit unfamiliar websites. Especially do not click on unknown links or attachments in emails that you receive from sketchy senders. Also be careful when clicking links in google searches. Disable java in the web browser that you use for general-purpose browsing, email, google searches, etc. Here are instructions for disabling java in a particular browser. Use a different browser for resources that require Java. Windows users: Due to a limitation in Internet Explorer, you should use Internet Explorer for java. Use a different browser such as Firefox or Chrome for general web browsing, and disable java in that browser. Disabling java in Firefox is not really necessary. The browser will simply wait to start it until you request it to do so, which is safe to do for Jmol sites. These recommendations were made by Michael Horowitz in his Defensive Computing Blog in his January 2013 post How to be as safe as possible with Java.
The list below contains modeling tutorial files that are available from Biochemistry Online: An Approach Based on Chemical Logic. Some are links to outside files, but the majority have been created specifically for this course, some by students.
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Chapter 1: Lipid Structure |
| di-18:0 PC |
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Chapter 2: Protein Structure |
| Amino Acids |
| RhoA - a cytoplasmic protein - The complexity of protein analysis |
| An isolated helix from an Antifreeze Protein |
| Twisted beta sheet |
| Beta barrel from triose phosphate isomerase |
| Reverse Turn Trypsin Inhibitor |
| helix-loop-helix from the lambda repressor/DNA |
| helix-loop-helix (EF Hand) from calmodulin |
| beta-hairpin from bovine pancreatic trypsin inhibitor |
| beta-helix-beta motif from triose phosphate isomerase |
| cytochrome B562 |
| met-myoglobin |
| triose phosphate isomerase |
| hexokinase |
| superoxide dismutase |
| human IgG1 antibody |
| retinol binding protein |
| RNase A |
| Apolactalbumin (w/o Ca2+)/Hololactalbumin |
| Engrailed homeodomain - denatured and native states |
| GroEL/ES |
| Cyclophilin |
| SecYEB Protein Translocase |
| Top7 - A designed 93 amino acid protein with a novel fold |
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Chapter 4: DNA, Genomics, and Proteomics |
| DNA Tutorial |
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Chapter 6: Transport and Kinetics |
| Lactose Permease |
| Glycerol-3-Phosphate Transporter From E. Coli |
| Aquaporin |
| Aquaporin Monomer |
| Valinomycin |
| Gramicidin |
| Maltoporin Transport Protein |
General Sites
General Jmol Sites