Biochemistry Online: An Approach Based on Chemical Logic

Jmol Files


New12/18/13:  I have just started updating these files to Jmol 14/JSmol.  Updated files are denoted by the phrase:

Updated Jmol14 (Java) |  JSMol  (HTML5).   With time, they will all eventually be updated.

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, 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.


Chapter 1:  Lipid Structure

conformations of ethane

conformations of propane

butane: the gauche conformation

di-18:0 PC


Updated Micelle  Jmol14 (Java) |  JSMol  (HTML5) 

Updated Nonhydrated Bilayer  Jmol14 (Java) |  JSMol  (HTML5) 

Human serum albumin  complex with 18:0


Chapter 2:  Protein Structure

Amino Acids
RhoA - a cytoplasmic protein - The complexity of protein analysis
Updated An isolated helix from an Antifreeze Protein  Jmol14 (Java) |  JSMol  (HTML5) 
Updated  Twisted beta sheet from Arabinose Binding Protein Jmol14 (Java) |  JSMol  (HTML5) 
Beta barrel from triose phosphate isomerase
Reverse Turn   Trypsin Inhibitor
Updated Lambda Repressor/DNA complex  Jmol14 (Java) |  JSMol  (HTML5)
helix-loop-helix (EF Hand) from calmodulin
beta-hairpin from bovine pancreatic trypsin inhibitor
beta-helix-beta motif from triose phosphate isomerase
cytochrome B562
Updated  met-myoglobin  Jmol14 (Java) |  JSMol  (HTML5) 
Updated  triose phosphate isomerase Jmol14 (Java) |  JSMol  (HTML5) 
Updated   superoxide dismutase Jmol14 (Java) |  JSMol (HTML5)   
human IgG1 antibody
 retinol binding protein
RNase A
Apolactalbumin (w/o Ca2+)/Hololactalbumin
Engrailed homeodomain - denatured and native states
SecYEB Protein Translocase
Top7 - A designed 93 amino acid protein with a novel fold

Prion Protein, Mad Cow Disease, and Mutations


Chapter 3:  Carbohydrates

D Glucose
Acetal Formation
Peptidoglycan glycosyl transferase
N-linked Glycoprotein
Oseltamivir (Tamiflu): Neuramindase N1 complex
P-Selectin Lectin/EGF Domains (IG1Q


Chapter 4:  DNA, Genomics, and Proteomics

DNA Tutorial


Chapter 5:  Binding

Avidin:Biotin Complex (1AVD)
Cu(I) Form Of E. Coli Cuer, A Copper Efflux
deoxy-heme and carbon monoxide-heme
Symmetry in Protein Oligomers (beta version with lots of work left to do)
Unliganded gp120 core (HIV viral protein)
Parainfluenza Virus 5F Protein
Updated Simple DNA Tutorial  Jmol14 (Java) |  JSMol  (HTML5)
TATA Box Binding Protein
RNA Polymerase II/DNA/RNA complex
Auxin Receptor
Updated Zif268:DNA Complex  Jmol14 (Java) |  JSMol  (HTML5)   
Updated   Lambda Repressor: DNA complex | Jmol14 (Java) |  JSMol  (HTML5) 
Updated Zif268:DNA Complex  Jmol14 (Java) |  JSMol  (HTML5)   
Leucine Zipper
Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA
Updated Nucleosome  Jmol14 (Java) |  JSMol  (HTML5)
TLR3:dsRNA complex
 Nf-Kb(P50)2 Complexed To A High- Affinity RNA Aptamer


Chapter 6:  Transport and Kinetics

Lactose Permease
Glycerol-3-Phosphate Transporter From E. Coli
Aquaporin Monomer
Maltoporin Transport Protein


Chapter 7:  Catalysis

Immunoglobulin 48G7 Germline Fab Antibody Complexed With Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid
Carboxypeptidase A
Chymotrypsin:D-Leu-L-Phe-p-fluorobenzylamde complex
Chymotrypin-Phenylethylboronate Inhibitor Complex
Comparison of Chymotrypin and Subtilisin
E. Coli GlpG rhomboid intramembrane protease
Mammalian Proteasome  - (1IRU)
Glyceraldehyde-3-phosphate dehydrogenase (NAD)
Self-splicing Group I intron with both exons
L1 Ligase Ribozyme
Puckering in ribose and deoxyribose
Comparison of ds DNA forms
Comparison of ds DNA and dsRNA


Chapter 8:  Oxidative Phosphorylation

Adenine DNA glycosylase:8-oxyG DNA complex
Flavin dehydrogenase
Estrogen Receptor Complexed Tamoxifen
Cytochrome P450cam
Cytochrome C Oxidase
Glyceraldehyde-3-phosphate dehydrogenase
Cytochrome C Oxidase
Succinate Dehydrogenase (Complex II)
Light Harvesting Complex from Spinach 1RWT
Detailed Photosystem II from S. elongatus
Photosystem I: A Photosynthetic Reaction Center and Core Antenna System From Cyanobacteria 1JBO


Chapter 9:  Energy and Signal Transduction

Bacteriorhodopsin Crystallized From Bicelles
EmrE multidrug resistance transporter
Updated Acetylcholine Receptor Pore  Jmol14 (Java) |  JSMol  (HTML5)  (1OED)
Potassium Channel
Updated Mammalian Voltage-Dependent Shaker Family Potassium Channel  Jmol14 (Java) |  JSMol  (HTML5)
Updated Chloride Channel   Jmol14 (Java) |  JSMol  (HTML5)
Updated Gs-alpha/adenylate cyclase complex   Jmol14 (Java) |  JSMol  (HTML5) 
Updated Beta andrenergic receptor  Jmol14 (Java) |  JSMol  (HTML5)  
Updated Beta andrenergic receptor:Gs Complex  Jmol14 (Java) |  JSMol  (HTML5)  
Updated  Melancortin 4 Receptor  Jmol14 (Java) |  JSMol  (HTML5)
Updated AMP-dependent Protein Kinase (AMPK)  Jmol14 (Java) |  JSMol  (HTML5)

General Sites

General Jmol Sites