Biochemistry Online: An Approach Based on Chemical Logic

Jmol Files


New6/10/14  With a few exceptions (which are bit difficult to convert), all of the Jmol files below (except those designated as external which are out of my control) are updated to Jmol 14 and JSMol.  JSmol does not require the Java plugin and hence can be viewed in any browser and on any device.  Rotation and upload speeds are slowed however when JSmol is used.

Updated Jmol14 (Java) |  JSMol  (HTML5)

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

Updated di-18:0 PC  Jmol14 (Java) |  JSMol  (HTML5) 

Updated Triacylglyceride  Jmol14 (Java) |  JSMol  (HTML5)

Updated Micelle  Jmol14 (Java) |  JSMol  (HTML5) 

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

Updated Human serum albumin complex with 18:0   Jmol14 (Java) |  JSMol  (HTML5)


Chapter 2:  Protein Structure

Amino Acids
Updated RhoA - a cytoplasmic protein - The complexity of protein analysis    Jmol14 (Java) |  JSMol (HTML5) 
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
Updated  Reverse Turn: Trypsin Inhibitor Jmol14 (Java) |  JSMol  (HTML5)
Updated  A protein with a buried nonpolar amino acid  Jmol14 (Java) |  JSMol  (HTML5) 
Updated helix-loop-helix of the lambda Repressor Jmol14 (Java) |  JSMol  (HTML5)
Updated  helix-loop-helix (EF hand) from calmodulin   Jmol14 (Java) |  JSMol  (HTML5)
Updated  beta-hairpin from bovine pancreatic trypsin inhibitor   Jmol14 (Java) |  JSMol  (HTML5)
Updated  beta-helix-beta motif from triose phosphate isomerase   Jmol14 (Java) |  JSMol  (HTML5)
Updated cytochrome B562  Jmol14 (Java) |  JSMol  (HTML5)
Updated  met-myoglobin  Jmol14 (Java) |  JSMol  (HTML5) 
Updated  triose phosphate isomerase Jmol14 (Java) |  JSMol  (HTML5) 
Updated  hexokinase Jmol14 (Java) |  JSMol  (HTML5) 
Updated   superoxide dismutase Jmol14 (Java) |  JSMol (HTML5)   
Updated   human IgG1 antibody Jmol14 (Java) |  JSMol (HTML5)  
Updated   retinol binding protein Jmol14 (Java) |  JSMol (HTML5)
Updated RNase A  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Apolactalbumin (w/o Ca2+)/Hololactalbumin   Jmol14 (Java) |  JSMol  (HTML5)
Updated Engrailed homeodomain - denatured and native state   Jmol14 (Java) |  JSMol  (HTML5) 
Updated   GroEL/ES   Jmol14 (Java) |  JSMol  (HTML5) 
Updated   Cyclophilin   Jmol14 (Java) |  JSMol  (HTML5) 
Updated   SecYEB Protein Translocase   Jmol14 (Java) |  JSMol  (HTML5)
 Updated  Top7 - A designed 93 amino acid protein with a novel fold    Jmol14 (Java) |  JSMol  (HTML5)

Updated   Prion Protein, Mad Cow Disease, and Mutations    Jmol14 (Java) |  JSMol  (HTML5)


Chapter 3:  Carbohydrates

Updated   β-D-glucopyranose    Jmol14 (Java) |  JSMol  (HTML5)
D Glucose
Acetal Formation
Updated  Peptidoglycan glycosyl transferase    Jmol14 (Java) |  JSMol  (HTML5)
N-linked Glycoprotein
Updated  Oseltamivir: Neuramindase N1 complex    Jmol14 (Java) |  JSMol  (HTML5)
Updated  P-Selectin Lectin/EGF Domains (IG1Q)    Jmol14 (Java) |  JSMol  (HTML5)


Chapter 4:  DNA, Genomics, and Proteomics

DNA Tutorial


Chapter 5:  Binding

Updated  Avidin:Biotin Complex (1AVD)   Jmol14 (Java) |  JSMol  (HTML5)
Updated  Cu(I) Form Of E. Coli Cuer, A Copper Efflux Regulator  Jmol14 (Java) JSMol  (HTML5)
Updated  deoxy-heme and carbon monoxide-heme Jmol14 (Java) JSMol  (HTML5)
Updated  Met-Myoglobin Jmol14 (Java) JSMol  (HTML5)
Updated  Symmetry in Protein Oligomers (beta version with lots of work left to do)  Jmol14 (Java) JSMol  (HTML5)  (button no show)
Unliganded gp120 core (HIV viral protein)  FIX
Updated  Parainfluenza Virus 5F Protein   Jmol14 (Java) JSMol  (HTML5)
Updated Simple DNA Tutorial  Jmol14 (Java) |  JSMol  (HTML5)
Updated  TATA Box Binding Protein   Jmol14 (Java) JSMol  (HTML5)
Updated  RNA Polymerase II/DNA/RNA complex   Jmol14 (Java) JSMol  (HTML5)
Updated  Auxin Receptor   Jmol14 (Java) JSMol  (HTML5)    Auxin Receptor
Updated   Lambda Repressor: DNA complex | Jmol14 (Java) |  JSMol  (HTML5) 
Updated Zif268:DNA Complex  Jmol14 (Java) |  JSMol  (HTML5)   
Updated Leucine Zipper  Jmol14 (Java) |  JSMol  (HTML5)
Updated Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA  Jmol14 (Java) |  JSMol  (HTML5)
Updated Nucleosome  Jmol14 (Java) |  JSMol  (HTML5)
dsRNA (still figuring out to convert to JSMol)
Updated Dicer  Jmol14 (Java) |  JSMol  (HTML5)   Dicer
Updated TLR3:dsRNA complex Jmol14 (Java) |  JSMol  (HTML5)  Needs updating
Updated Nf-Kb(P50)2 Complexed To A High- Affinity RNA Aptamer Jmol14 (Java) |  JSMol  (HTML5)


Chapter 6:  Transport and Kinetics

Updated Lactose Permease Jmol14 (Java) |  JSMol  (HTML5)
Updated  Glycerol-3-Phosphate Transporter From E. Coli Jmol14 (Java) |  JSMol  (HTML5)
Updated  Aquaporin Monomer Jmol14 (Java) |  JSMol  (HTML5)
Updated  Maltoporin Transport Protein Jmol14 (Java) |  JSMol  (HTML5)


Chapter 7:  Catalysis

Updated  Immunoglobulin 48G7 Germline Fab Antibody Complexed With Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid   Jmol14 (Java)  JSMol  (HTML5) 
Updated Carboxypeptidase A Jmol14 (Java) |  JSMol  (HTML5) 
Updated Chymotrypsin:D-Leu-L-Phe-p-fluorobenzylamde complex  Jmol14 (Java) |  JSMol  (HTML5)
Updated Chymotrypin-Phenylethylboronate Inhibitor Complex  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Comparison of Chymotrypin and Subtilisin  Jmol14 (Java) |  JSMol  (HTML5) 
Updated E. Coli GlpG rhomboid intramembrane protease  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Mammalian Proteasome  - (1IRU)   Jmol14 (Java) |  JSMol  (HTML5)
THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE (1pyd)  (go to left hand Display Molecule, choose Jmol viewer).
Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD)   Jmol14 (Java) |  JSMol  (HTML5) 
Tyrosine Aminotransferase  Jmol  (from PDB)
Updated Self-splicing Group I intron with both exons   Jmol14 (Java) |  JSMol  (HTML5)  
Updated L1 Ligase Ribozyme   Jmol14 (Java) |  JSMol  (HTML5)  Not done; Fix
Puckering in ribose and deoxyribose  Not updated Fix
Comparison of ds DNA forms  Not updated Fix
Comparison of ds DNA and Not updated Fix


Chapter 8:  Oxidative Phosphorylation

Updated Adenine DNA glycosylase:8-oxyG DNA complex  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Flavin dehydrogenase  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Estrogen Receptor:Tamoxifen Complex   Jmol14 (Java) |  JSMol  (HTML5) 
Updated Cytochrome P450cam  Jmol14 (Java) |  JSMol  (HTML5) 
Cyclooxygenase I and II
Updated Cytochrome C Oxidase   Jmol14 (Java) |  JSMol  (HTML5) 
Updated ATP  Jmol14 (Java) |  JSMol  (HTML5)    |   ADP  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD)   Jmol14 (Java) |  JSMol  (HTML5) 
Updated Cytochrome C Oxidase   Jmol14 (Java) |  JSMol  (HTML5) 
Updated Succinate Dehydrogenase (Complex II)    Jmol14 (Java) |  JSMol  (HTML5) 
Updated Light Harvesting Complex from Spinach 1RWT     Jmol14 (Java) |  JSMol  (HTML5) 
Updated Detailed Photosystem II from S. elongatus  Jmol14 (Java) |  JSMol  (HTML5) 
Updated Photosystem I: A Photosynthetic Reaction Center and Core Antenna System From Cyanobacteria 1JBO   Jmol14 (Java) |  JSMol  (HTML5) 


Chapter 9:  Energy and Signal Transduction

Updated Bacteriorhodopsin Crystallized From Bicelles   Jmol14 (Java) |  JSMol  (HTML5)        |  LMW-PTP isoform A
Updated EmrE multidrug resistance transporter   Jmol14 (Java) |  JSMol  (HTML5)
Updated Acetylcholine Receptor Pore  Jmol14 (Java) |  JSMol  (HTML5)  (1OED)
Potassium Channel  Not updated; Needs work
Updated Mammalian Voltage-Dependent Shaker Family Potassium Channel  Jmol14 (Java) |  JSMol  (HTML5)
Updated Chloride Channel   Jmol14 (Java) |  JSMol  (HTML5)
NEW Low molecular weight protein tyrosine phsophatase 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