World Index:
BioMolecular Tutorials in Chime by Subject

To view a tutorial listed below, visit the web site of its author(s). If you know of a tutorial not listed here, please email the URL to me. Documents about Chime and how to use it are in brown. For help on using RasMol, see the RasMol Home Page.

Not indexed here are the Molecules of the Month, a series of short Chime presentations. Separate series on different molecules are available from Imperial College, London UK, the University of Oxford UK, and the University of Bristol UK. See also MDL's Chime Cool Examples listing which has many chemistry tutorials not included here.

• Alkaline protease of Pseudomonas aeruginosa, zinc active site, eight calciums, five in a beta-sandwich ("beta coil", "beta helix"). Grisham & O'Neil.
• Alpha helix: see protein secondary structure.
• Alpha helix: myoglobin. Helmkamp & Grant.
• Amino acids with detailed properties. Gasser.
• Amino acids with image-based quiz. McClure.
• Amino acids, see peptide bond.
• Animations (molecular dynamic): pharmaceuticals, also PDB's with double bonds. Dobashi.
• Antibody binding to antigen lysozyme, with intro to protein structure and representations, Ig domains, CDR's. Aussi en Français. Martz.
• Antibody, see immunoglobulin.
• Antigen presentation, see major histocompatibility complex.
• A-RNA helix McClure.

• B-DNA helix McClure.
• Bacteriorhodopsin of Halobacterium halobium. Dewhurst.
• Beta helix, beta coil, beta sandwich, see alkaline protease.
• Beta sheet: fatty acid binding protein. Helmkamp & Grant.
• Beta-sheet protein:DNA interactions (E. coli Met repressor) Driscoll.
• Buckminsterfullerence (C₆₀: Inorganic crystal) Maverick.

• Calcium binding EF hand morph. Martz.
• Calcium fluoride (Inorganic crystal) Maverick.
• Calmodulin morph. Martz.
• Carbon (Diamond & Buckminsterfullerene: Inorganic crystal) Maverick.
• Carbon nitride (Inorganic crystal) Maverick.
• Catalase Marcey, Boon & Downs.
• CD4, showing binding site for HIV-1 gp120 Dewhurst
• Cesium Chloride (Inorganic crystal) Maverick.
• Chemotaxis Y protein (CheY, alpha/parallel beta w/ Mg⁺⁺) McClure.
• Chime: command-line interface, sample showing how to implement. Martz.
• Chime: creating web pages for (chemical script, HTML, javascript). Martz.
• Chime: manual for script command enhancements and HTML/javascript controls. Maffett.
• Chime: mouse controls, see mouse controls.
• Chime vs. RasMol for educational tutorials. Martz.
• Cholesterol, see lipid bilayer.
• Citric acid cycle. Helmkamp & Grant.
• Citric acid cycle, see tricarboxylic acid cycle.
• Copper (Inorganic crystal structure) Maverick.
• Crystals: Inorganic Maverick.
• cyclic-AMP receptor protein McClure.
• Cyclooxygenases and the mechanism of action of aspirin/NSAID's. Grisham & O'Neil.
  ABC   DEF   GHI   JKL   MNO   PQR   STU   VWXYZ

• Diamond (Inorganic crystal) Maverick.
• DNA B-form helix McClure.
• DNA-binding proteins: see lac repressor; glucocorticoid receptor.
• DNA double helix structure, base pairing and hydrogen bonding. Aussi en Français. Martz.
• DNA double helix, base pairing, antiparallelism. Nonlinear interactive tutorial. Martz.
• DNA polymerase III, beta subunit, E. coli Marcey.
• DNA-protein interactions, binding motifs. Driscoll.
• DNA topoisomerase, see topoisomerase.

• EF hand morph. Martz.
• Elongation factor Tu, tRNA^Phe, and GTP McClure.
• Elongation factor-Tu protein:RNA interactions (yeast EF-Tu) Driscoll.

• Fatty acid binding protein, see beta sheet.
• FeCr₂O₄ (Inorganic crystal) Maverick.
• Ferredoxin. Nakai.
• Flavodoxin (alpha/parallel beta) Grisham & O'Neil.
• Fyn Src homology 3 (SH3) domain, see HIV-1 Nef.
  ABC   DEF   GHI   JKL   MNO   PQR   STU   VWXYZ

• Gal4 transcriptional regulating protein of yeast McClure.
• G proteins Grisham & O'Neil.
• G proteins Helmkamp & Grant.
• Glycolysis pathway intermediates. McClure.
• Glucocorticoid receptor/zinc finger binding to DNA. Brzeski.
• Gramicidin, see lipid bilayer.

• Helix-turn-helix DNA-binding protein, see lac repressor.
• Helix-turn-helix protein:DNA interactions (phage Trp repressor) Driscoll.
• Hemoglobin, heme, hydrophobic core, sickle mutation and polymerization. Martz.
• Hin Recombinase of Salmonella, DNA-binding domain Marcey, Millard & Downs.
• HIV-1 Integrase catalytic core domain & minimal DNA binding domain Marcey & Walsh.
• HIV-1 Nef complexed with Src-family SH3 domain. Dewhurst
• HIV-1 protease. Grisham & O'Neil.
• HIV-1 protease showing active site, binding site for indinavir. Dewhurst
• HIV-1 reverse transcriptase. Marcey & Goldman.
• HLA, see major histocompatibility complex.
• hnRNP-A1, human McClure.

• Immunoglobulin and protein domains. Helmkamp & Grant.
• Immunoglobulin, see antibody.
• Inorganic crystals Maverick.
• Integrase of HIV-1, catalytic core domain & minimal DNA binding domain Marcey & Walsh.

• Javascript, use with Chime, see Chime, creating web pages for.

• Krebs cycle, see citric acid cycle, see tricarboxylic acid cycle.

• Lac repressor binding to DNA. Fragment of helix-turn-helix protein. Brzeski.
• Leucine zipper protein:DNA interactions (yeast GCN4) Driscoll.
• Lipid bilayer, 200-phosphatidyl choline bilayer embedded in water. Cholesterol shown but not in bilayer. Gramicidin in bilayer with water in channel. Martz.
• Lysozyme, see protein secondary structure.
  ABC   DEF   GHI   JKL   MNO   PQR   STU   VWXYZ

• Major histocompatibility complex (MHC) with peptide binding showing different virus epitopes. Aussi en Français. Martz.
• Manual for script command enhancements and HTML/javascript controls, see Chime: manual.
• Membrane and membrane channel, see lipid bilayer.
• Miscellaneous small biological molecules. Lancashire.
• Morphs: Protein. Martz.
• Mouse controls in Chime, how to use them (rotation, translation, zoom, slab). Martz.
• MS2 Capsid protein:RNA interactions (viral coat protein) Driscoll.
• Mutation, see hemoglobin, DNA.
• Myoglobin, an oxygen-binding alpha protein. Helmkamp & Grant.
• Myoglobin, see alpha helix.

• Noncovalent bond finder for ligand-protein interactions (works on the protein of your choice). Martz.

• p53 tumor suppressor. Grisham & O'Neil.
• PbTiO₃ (Inorganic crystal) Maverick.
• Peptide bond and amino acids. Helmkamp & Grant.
• Pharmaceuticals, double-bond PDB's with molecular dynamic animations. Dobashi.
• Phosphotyrosine, see src.
• Prostaglandin H synthase, see cyclooxygenase. Grisham & O'Neil.
• Photosynthetic reaction center from purple bacteria. Nixon, Leach & Rzepa
• Protease, alkaline, of Pseudomonas aeruginosa, see alkaline protease.
• Protein: Morphs. Martz.
• Protein G, see protein secondary structure.
• Protein kinase C. Grisham & O'Neil.
• Protein-Nucleic acid interactions: binding motifs. Driscoll.
• Protein secondary structure, lysozyme, for 10 min lecture. Martz.
• Protein secondary structure, protein G, with image-based quiz. McClure.
• Protein secondary structure, see alpha helix, see beta sheet.

• RANTES beta chemokine (inhibits infection of T cells by HIV). Dewhurst
• RasMol script writing, see scripting.
• RasMol vs. Chime, see Chime vs. RasMol.
• Recombinase, Hin, of Salmonella, DNA-binding domain Marcey, Millard & Downs.
• Recoverin morph. Martz.
• ReO₃ (Inorganic crystal) Maverick.
• Reverse transcriptase, see HIV-1 reverse transcriptase.
• RNA A-form helix McClure.
• RNA-protein interactions, binding motifs. Driscoll.
• RNA, transfer, yeast, Phe. McClure.
  ABC   DEF   GHI   JKL   MNO   PQR   STU   VWXYZ

• Scripting guide for RasMol and Chime. Martz
• Scripting tutorial for Chime and RasMol. Miller
• Secondary structure, see protein secondary structure.
• Seven-transmembrane receptors, see Bacteriorhodopsin.
• snRNP-U1A McClure.
• Sodium Chloride (Inorganic crystal) Maverick.
• Src homology 2 (SH2) domain of phospholipase C gamma 1 binding to phosphotyrosine peptide. Martz.
• Src homology 2 (SH2) domain of Syk binding to phosphotyrosine peptide. Dewhurst. Intact Syk (not shown) includes a second SH2 domain and a tyrosine kinase domain, and binds to immunoreceptor tyrosine-based activation motifs (ITAMs) on the CD2/T cell receptor complex.
• Src homology 3 (SH3) domain, see HIV-1 Nef.
• Syk, see Src homology 2 (SH2) domain of Syk.

• Tat protein:RNA interactions (BIV transactivator) Driscoll.
• Thermal motion of alpha helix, molecular dynamics simulation. Cachau.
• TiO₂ (Inorganic crystal) Maverick.
• Topoisomerase I. Marcey & Kysela.
• Tricarboxylic Acid (TCA) cycle pathway intermediates. McClure.
• Tricarboxylic Acid (TCA) cycle, see citric acid cycle.
• tRNA, see RNA, transfer.

• U1A snRNP protein:RNA interactions (human splicing factor) Driscoll.

• YBa₂Cu₃O₇ (Inorganic crystal) Maverick.
• Zinc (Inorganic crystal) Maverick.
• Zinc in protease active site, see alkaline protease.
• Zif268 Zinc Finger McClure.
• Zinc finger binding to DNA, see glucocorticoid receptor.
• Zinc finger protein:DNA interactions (E. coli Gal4) Driscoll.
• Zinc sulfide (Inorganic crystal) Maverick.

• Brzeski, Henry, University of Strathclyde, Glasgow UK. These presentations go into considerable detail about the chemical bonds between protein and DNA.
  Chime Tutorials
  • Lac repressor binding to DNA. Fragment of helix-turn-helix protein.

    RasMol "movie" scripts

  • Lac repressor binding to DNA. Fragment of helix-turn-helix protein.
  • Glucocorticoid receptor/zinc finger binding to DNA.

• Cachau, Raul, Frederick Cancer Research Facility of the National Cancer Institute, Frederick MD US.
  • Thermal motion of alpha helix, molecular dynamics simulation.

• Dewhurst, Steve, U Rochester Medical Center, Rochester NY US.
  • Bacteriorhodopsin.
  • CD4, showing binding site for HIV-1 gp120.
  • HIV-1 Nef complexed with Src family SH3 domain.
  • HIV-1 protease showing active site, binding site for indinavir.
  • RANTES beta chemokine (inhibits infection of T cells by HIV).
  • Syk SH2 domain complexed to phosphotyrosine peptide.

• Dobashi, Akira, and George Georgalis, Tokyo University of Pharmacy and Life Science, JP. This site has PDB files for thousands of pharmaceuticals, with double bonds, shown in Chime. It also has molecular dynamic animations of all these molecules!

• Driscoll, Tim, U Mass & Amherst College, Amherst MA US. Press the red balls to move around in this excellent tutorial on protein:nucleic acid contacts which includes both DNA and RNA examples:
  • zinc finger (E. coli Gal4)
  • helix-turn-helix (phage Trp repressor)
  • leucine zipper (yeast GCN4)
  • b-sheet (E. coli Met repressor)
  • EF-Tu (yeast elongation factor)
  • U1A snRNP (human splicing factor)
  • MS2 Capsid (viral coat protein)
  • Tat (BIV transactivator)

• Gasser, Charles S., U California Davis CA US.
  • Amino acids with detailed properties.

• Grisham, Charles M., and Edward K. O'Neil, University of Virginia, Charlottesville VA US. At this site, select the link Studying protein structures with Chemscape Chime.
  • Cyclooxygenases and the mechanism of action of aspirin/NSAID's.
  • Flavodoxin
  • G proteins
  • HIV-1 protease.
  • p53 tumor suppressor
  • Protein kinase C
  • Alkaline protease of Pseudomonas aeruginosa (zinc, 8 calcium- "beta helix")

• Helmkamp, George, and John R. Grant, U Kansas Medical Center, Kansas City KS US. These Chime presentations were written prior to the release of Chime 1.0, so do not make use of some of Chime's newer features. As of April, 1997, these tutorials cannot be viewed on a 1024x768 Windows 3.1x/Netscape 3.01 screen due to a bug which prevents the forward button from being accessible; they can be viewed on an 800x600 Windows screen.
  • Alpha helix: myoglobin.
  • Beta sheet: fatty acid binding protein.
  • Citric acid cycle.
  • G proteins.
  • Immunoglobulin and protein domains.
  • Myoglobin, an oxygen-binding protein.
  • Peptide bond and amino acids.

• Lancashire, Robert, U West Indies, Mona Campus, JM.
  • Miscellaneous small biological molecules.

• Maffett, Tim MDL Information Systems, Inc., San Leandro CA US. Tim Maffett is the principal architect and primary programmer for Chime.
  • Chime: manual for script command enhancements and HTML/javascript controls.

• Marcey, David, et al., Kenyon College, Gambier OH US. These tutorials are unusually well documented with accompanying text, which not only introduces the subject clearly but also goes into some depth, with references.
  • Catalase (with Elizabeth M. Boon and Aaron Downs)
  • DNA polymerase III, beta subunit, E. coli
  • Hin Recombinase of Salmonella, DNA-binding domain (with Elizabeth E. Millard and Aaron Downs)
  • HIV-1 Integrase catalytic core domain & minimal DNA binding domain (with Matthew Bok Walsh)
  • HIV-1 reverse transcriptase (with Mathew Goldman)
  • Topoisomerase I (with David Kysela)

• Martz, Eric, University of Massachusetts, Amherst MA US. This Chime site has extensive help, manuals, and information about how to create Chime tutorials on the web. The tutorials make full use of the features of Chime 1.0, and often use javascript. This RasMol site has a guide to RasMol "movie" script creation, and the largest collection of RasMol information at any one web site. Quelques scripts ont été traduits en Français par l'Institut National de Recherche Pédagogique.
  Chime Tutorials
  • Antibody.
  • Chime: command-line interface, sample showing how to implement.
  • Chime: creating web pages for (chemical script, HTML, javascript).
  • Chime vs. RasMol for educational tutorials.
  • DNA double helix, base pairing, antiparallelism. Nonlinear interactive tutorial.
  • Hemoglobin
  • Major Histocompatibility Complex with bound viral peptides.
  • Noncovalent bond finder for any protein:ligand
  • Mouse controls in Chime, how to use them (rotation, translation, zoom, slab).
  • Protein secondary structure, lysozyme.
  • Protein morpher: Chime movies of configurational changes of Recoverin (including closeup of the effect of calcium on an EF Hand), Influenza Hemagglutinin, and CD11b Leukocyte Integrin MIDAS Adhesion Domain

    RasMol "movie" scripts

  • Antibody binding to antigen lysozyme, with intro to protein structure and representations, Ig domains, CDR's. Aussi en Français.
  • DNA double helix structure, base pairing and hydrogen bonding. Aussi en Français.
  • Hemoglobin, heme, hydrophobic core, sickle mutation and polymerization.
  • Lipid bilayer, 200-phosphatidyl choline bilayer embedded in water. Cholesterol shown but not in bilayer. Gramicidin in bilayer with water in channel.
  • Major histocompatibility complex (MHC) with peptide binding showing different virus epitopes. Aussi en Français.
  • Src homology 2 (SH2) domain of phospholipase C gamma 1 binding to phosphotyrosine peptide.

• Maverick, Andrew, Louisiana State University, Baton Rouge LA US.
  • Inorganic crystal structures.

• McClure, William, Carnegie-Mellon University, Pittsburgh PA US. These tutorials have considerable depth and also use Chime fully and creatively. Some of the quizzes are answered by clicking on an atom, an excellent innovation sure to be followed by others.
  Chime Tutorials
  • Amino acids with image-based quiz.
  • A-RNA helix
  • B-DNA helix
  • Chemotaxis Y protein (CheY, alpha/parallel beta w/ Mg⁺⁺)
  • cyclic-AMP receptor protein
  • Elongation factor Tu, tRNA^Phe, and GTP
  • gal4 protein of yeast
  • Glycolysis pathway intermediates.
  • hnRNP-A1, human
  • Protein secondary structure, protein G, with image-based quiz.
  • RNA, transfer, yeast, Phe.
  • snRNP-U1A
  • Tricarboxylic Acid (TCA) cycle pathway intermediates.
  • Zif268 Zinc Finger

    RasMol "movie" scripts

  • RNA, transfer, yeast, Phe.

• Miller, Mitchell, MDL Information Systems, Inc., San Leandro CA US.
  • Scripting tutorial for Chime and RasMol.

• Nakai, Masato, U Osaka JP.
  • Ferredoxin.

• Nixon, Peter, Christopher Leach and Henry S. Rzepa, Imperial College, London UK. Probably the first Chime tutorial presentation on the web (early 1996). Uses Chemical Script Markup Language (CSML), a simplified subset of RasMol command language.
  • Photosynthetic reaction center from purple bacteria: UK or US.