Molecular Cell Physiology - MCDB 3280
3280 Home
Following this list are links to
Chime-based tutorials on the Web
and
links to sites that display molecules in Chime format
and
links to information about Chime, Rasmol and Molecular Display
MCDB 3280 Student Projects:
Molecular Tutorials Presented in Chime Format

IMPORTANT NOTE ON CHIME BROWSER COMPATABILITY
a.k.a: It doesn't work With Every Browser and Platform

These tutorials utilize a program called Rasmol that itself utilizes a browser plug-in format known as Chime. Chime is developed and maintained as a non-commercial service by the commercial firm MDL Information Systems as described on their Chime Introduction Pages. Chime (and thus Rasmol) only works with some browser-platform combinations. this is described more fully by Eric Martz and on the MDL Chime compatability page. The current version of Chime is 2.6 (SP3). The following information is for current 2.6(SP3) version only.

Stated briefly, the situation as of August 2002 is as follows:

Windows 98/2000/NT PC Platforms
Chime works with Internet Explorer 5.5 (SP2) and 6 (and pretty well in 7).

Chime works with Netscape Communicator 4.75
There is no announcement when or whether a plug-in for more recent versions of Netscape will be available.

Macintosh PowerMac Platforms and Operating systems
Chime works with Netscape Communicator 4.75 running in Mac OS 8.x or 9.x
Some users have made Chime work with Netscape 6 and Mac OS 9.x
There is no announcement of when or whether a plug-in for more recent versions of Netscape and/or for Mac OS X will be available.

Chime does not work with Internet Explorer versions for the Macintosh.
Molecule Treated
Student Name
Semester
Acetylcholinesterase Christina Cowan
Sp 2000
Albumin Robb Freed
Fall 2001
Alcohol Dehydrogenase, Drosophila Natasha Surette
Sp 2000
Annexin 1 Brandon Schwarzentraub
Fall 2001
Antifreeze Protein, Winter Flounder Ashima Gupta
Fall 2001
Arginine-binding RNA Aptamer Jason Bobe
Sp 2000
cAMP-Dependent Protein Kinase Morgan Minyard
Fall 2001
beta-Catenin Mike Osgood
Fall 2001
CD4 Receptor Dale Cassidy
Sp 2000
Cellobiohydrolase I Ryan Hafen
Sp 2000
Chorionic Gonadotropin, Human Marybeth Maligie
Fall 2001
Clostridium Botulinum Neurotoxin Mark McCabe
Fall 2001
Cytochrome C Craig Fossee
Fall 2001
Cytochrome C Peroxidase Jeffrey Hoskins
Fall 2001
Dihydropteridine Reductase Sanlyn Buxner
Sp 2000
DNA TATA Binding Protein, eukaryote Sonemala Phommatha
Sp 2000
Ebola Virus Glycoprotein Andrea McReynolds
Sp 2000
EF-Tu bound with tRNA and GNP Robert Murphy
Sp 2000
Ferritiin Mark Lauricello
Fall 2001
Ferrochelatase Agnessa Gadeliya
Fall 2001
Glycolytic Pathway Obie Williams
Sp2000
Insulin Christopher Chacon
Sp 2000
Interkeukin 1 beta, human Matt Stark
Sp 2000
Nerve Growth Factor Dipesh Amin
Sp 2000
Nucleosome Core Particle Laila Strickland
Sp 2000
p53, tumor suppressor protein Chris Ratliff
Sp 2000
Phosophoglycerate Mutase Chris Lyons
Fall 2001
Porin, sucrose channel Tai Huu Nguyen 
Sp 2000
Potassium Channel KcsA Alan Blaher
Sp 2000
Rhinovirus 16, Human Lisa Nguyen
Fall 2001
Scorpion Neurotoxin P01 Katie Navratil
Fall 2001
SIR-2 David Conard
Fall 2001
Sonic Hedgehog Mary Atz
Sp 2000
TFIIIA and DNA and Zinc Finger Interactions Andrew Ryscavage
Sp 2000
Tropomyosin Lucy Golebiewska
Fall 2001
UvrB Excision Repair Protein Kelly Lusk
Fall 2001

Chime-based Biological-molecule Tutorials on the Web

This list links directly to the individual tutorials. It includes only molecules of biological interest and is limited mainly to extended, tutorial-type presentations, as opposed to simple molecular views. It was last updated September 2001).

Acetylcholinesterase (LC)
Acetylcholinesterase (UCB)
Adenosine Deaminase (LC)
Albumin (UCB)
Alcohol Dehydrogenase, Drosophila (UCB)
Alpha Hydroxysteroid/Dihydrodiol Dehydrogenase (LC)
Alkaline Protease: Beta Helix of Pseudomonas aeruginosa (UV)
Annexin 1 (UCB)
Anthranilate Synthase (LC)
Arginine-binding RNA Aptamer (UCB)
Antibody Recognition of Antigen (OMM)
Antifreeze Protein, Winter Flounder (UCB)
Antileucoproteinase (LC)
ATP Synthase
Bacteriorhodopsin (UR)
Bacteriorhodopsin (B3D)
BamH1 Restriction Endonuclease (OMM)
Bisphosphoglycerate-deoxy hemoglobin (UA)
Beta-BZ Crystalline Tetramer (LC)
Beta-Lactamase (LC)
cAMP Receptor Protein (CRP) (CMU)
Calmodulin (LC)
cAMP-Dependent Protein Kinase (UCB)
Catabolite Activating Protein, E. coli (KC)
Catabolite Gene Activator Protein (CAP) (LC)
Catalase (KC)
Catalase (OMM)
beta-Catenin (UCB)
CD4 Receptor (UCB)
Cellobiohydrolase I (UCB)
Chorionic Gonadotropin, Human (UCB)
Chymotrypsin
Chymotrypsin, a Serine protease (UA)
Chymotrypsin and Elastase: Serine protease evolution (UA)
Citrate Synthase (LC)
Clostridium Botulinum Neurotoxin (UCB)
Clotting Factor IX (LC)
CopG Plasmid Regulator (KC)
Cro Repressor of Bacteriophage (OMM)
Cry3Aa3 Toxin, Bacillus thuringiensis
Cyclooxygenases and the Mechanism of Action of Aspirin and NSAIDs (UV)
Cytochrome C (UCB)
Cytochrome Oxidase (UA)
Cytochrome C Peroxidase (UCB)
Dihydropteridine Reductase (UCB)
Dihydrofolate Reductase (LC)
DNA Helicase (LC)
DNA Helix, B -form (CMU)
DNA polymerase III: Beta-subunit of E. coli  (OMM)
DNA structure
DNA TATA Binding Protein, eukaryote (UCB)
Ebola Virus Glycoprotein (UCB)
EcoRI Res. Endonuclease (CMU)
EcoRV, Restriction Endonuclease (B3D)
EF-Tu (LC)
EF-Tu bound with tRNA and GNP (UCB)
EF-Tu, tRNAPhe, and GTP (CMU)
Estrogen Receptor Ligand Domain, and DNA-Binding Domain
Ferritiin (UCB)
Ferrochelatase (UCB)
Ferrodoxin
FGAR Amidotransferase structure function predictions (LC)
Fibronectin (KC)
Fibronectin (OMM)
F1-ATPase
Flavodoxin Crossovers from Anabaena (UV)
G Protein (B3D)
G Proteins - Molecular Nanomachines (UV)
GAL4 Protein (yeast)(CMU)
Gamma B Crystalline
Glucosamine-6-phosphate Synthase (LC)
Gli1 Zinc Finger Protein (LC)
Glycolytic Pathway (UCB)
Green Fluorescent Protein, part 1, part 2
Hammerhead Rybozyme (B3D)
Hemagglutinin Antigen of Flu Virus (OMM)
Hemoglobin 
Hemoglobin
Hemoglobin
Hemoglobin (KC)
Hemoglobin S (UA)
HhaI DNA Methylase (OMM)
Hhal DNA Methyl Transferase (KC)
HhaI Res. Methylase (CMU)
Hin Recombinase (KC)
Hin recombinase (OMM)
HIV-1 Aspartic Proteinase
HIV-1 Dimer initiation Complex (KC)
HIV-1 gp120 complexed to CD4 and antibody that blocks chemokine-receptor site (UR)
HIV-1 gp120 (OMM)
HIV-1 Integrase (OMM)
HIV-1 Nef (OMM)
HIV-1 Nef with discussion of protein function, kinase binding (UR)
HIV-1 Protease showing active site, and binding site for indinavir (UR)
HIV-1 Protease (UV)
HIV-1 Protease (OMM)
HIV-1 Protease (UA)
HIV-1 Reverse Transcriptase (KC)
HIV-1 Reverse Transcriptase (OMM)
hnRNP A1 (human)(CMU)
Immunoglobulin (UA)
Immunoglobin (OMM)
Immunoglobin 
Immunoglobin and Antigen (UA)
Immunoglobin Recognition of Antigen (OMM)
Influenza Hemagglutinin (KC)
Isocitrate Dehydrogenase (LC)
Insulin (UCB)
Insulin
Interkeukin 1 beta, human (UCB)
Kinesin (LC)
Lac repressor (B3D)
Lac repressor (UM)
Lac repressor binding to DNA. Fragment of helix-turn-helix protein
Lactose Repressor (KC)
Leucine Zipper (UM)
Lipase (UA)
Luciferase (LC)
Lysozyme (LC)
Lysozyme
Lysozyme (UA)
MHC Major Histocompatability Complex
MHC Molecules (B3D)
MHC I (LC)
MHC II (LC)
MunI Restriction Enzyme (LC)
MutH Mismatch Repair Enzyme (OMM)
MutS Mismatch Repair Enzyme (OMM)
Myoglobin and hemoglobin
Nerve Growth Factor (UCB)
Nitrogen Regulatory Protein C (OMM)
Nucleosome (CMU)
Nucleosome (UA)
Nucleosome Core Particle (UCB)
Nucleosome Core + DNA (LC)
Oxygen Binding Proteins (B3D)
p53, tumor suppressor protein (UCB)
P53-A Tumor Supressor Protein (UV)
Pax-6 Transcription Factor (Human) (LC)
Pepsin
Phosophoglycerate Mutase (UCB)
Photosystem II Core
Porin (UA)
Porin, sucrose channel (UCB)
Porins (KC)
Porins: OMPF and Maltoporin (LamB) (E. coli) (OMM)
Porphorins, non-planer, comprehensive lectures and images
Potassium Channel KcsA (LC)
Potassium Channel KcsA (UCB)
Procathepsin K (LC)
Protein Disulfide Oxidoreductase (LC)
Protein Kinase C (UV)
Protein Tyrosine Phosphatase 1B (OMM)
PRPP-Glutamine amidotransferase (LC)
RANTES (human), beta chemokine, inhibits infection of T cells by M-tropic HIV-1 strains (UR)
Ras GTPase (LC)
Ras Proteins
Ras-Son of Sevenless Interaction (LC)
RecA (E. coli) (OMM)
Renin (LC)
Rhinovirus 16 human (UCB)
Rhodopsin (UA)
RNA Helix, A-form (CMU)
SCD4 (human) showing binding site for HIV-1 gp120 (UR)
Scorpion Neurotoxin P01 (UCB)
Serine Proteases (UA)
Serine Protease Evolution (UA)
Sesquiterpene Cyclase (LC)
Signal Recognition Particle Core of E. coli (OMM)
SIR-2 (UCB)
snRNP U1A (CMU)
Sonic Hedgehog (UCB)
src Tyrosine Kinase (LC)
Syk Tyrosine Kinase protein kinase involved in T cell activation and signal transduction (UR)
T7 DNA Ligase (LC)
T7 DNA Replication Complex (OMM)
T7 DNA Polymerase (KC)
TATA Binding Protein (LC)
Taq Polymerase (LC)
Tc3 Transposase Protein (C. elegans) (KC)
Transcription Factor IIIA and DNA and Zinc Finger Interactions (UCB)
Transcription Factors (UA)
Topoisomerase I (KC)
Topoisomerase I (E. coli) (OMM)
Transforming Protein P21/H-ras-1 (LC)
tRNA and seryl-tRNA Synthetase (KC)
Transmembrane Proteins (UA)
Tropomyosin (UCB)
Troponin C (LC)
Triosephosphate Isomerase (UA)
Trypsin inhibitor (UA)
Trypsin and Inhibitor (LC)
Trypsin and Trypsinogen: Zymogens (UA)
Tubulin (LC)
U1A Splicosomal Proteins (OMM)
UvrB Excision Repair Protein (UCB)
Viral Antigens (OMM)
Zinc Finger (UM)
Zinc finger Zif268 (CMU)
Zymogens (UA)

Links to sites with significant numbers of individual organic molecules

Includes molecules such as small peptides, organic molecules and pharmaceuticals, as well as some basic biochemistry bonding and amino acid tutorials. Some are directly in Chime and others are PDB files that can be viewed using Chime.

Links to sites that deal with Chime, Rasmol and Molecular Display

These Sites are GREAT Starting Points

Molecular Visualization Resources
THE comprehensive compendium that is continuously updated.
Chime Plug-in Download site.
This is the place to get the browser plug-in that runs Chime displays. They also maintain a Chime Great Sites list.
Chime Plug-in Demo.
Briefly explains all of the features of a Chime-based display
RasMol: Downloading and Installing & Chime Information
RasMol is molecule display software that was a precursor to Chime and that is used for authoring displays than can be viewed using Chime. Eric Martz, who has done significant work in making Rasmol accessible to faculty and students, maintains this wonderful, comprehensive site. Including a Where To Get molecules list more comprehensive than this one. Eric Martz also is developing a newer display tool, Protein Explorer.
PDBLite
One of the standard and easiest tools to search for and download any Brookhaven Protein Data Bank (PDB) file. USA mirror site, England mirror site, Israel mirror site, India mirror site.
Molecules-R-Us
A comprehensive collection of actual structures. A WWW interface that facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB).

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