Molecular Visualization for Project VISM

Molecular Visualization Resource Page
Welcome Back to VISM 2003:
New links for you to try:
RasTop (This is a drop-down menu version of RasMol.)
Comparison of Five Chemical Drawing Programs
PDB to MultiGif Converter

Shortcuts to Navigate this page:
New Links
Example Pages
Pages you can use as templates for your own Chime projects
An assortment of pdb and other molecular structure files
More molecules
Online Handouts
Exploring RasMol and Chemscape Chime
You can download and print a copy of the RasMol Quick Reference Card from this site
Where to find pdb and mol files
Chemscape Chime Example
Lesson Plans for Small Molecules
Case Example: Create your own Interactive Web Site for the Bowen's Reaction Series
Customized Molecular File Collections
Web Resources for Molecular Visualization
New Links (as of July 16, 2002):
Using Chime to illustrate spectral vibrations.
World Index of Molecular Visualization Resources
(I asked them to add the K-12 section, but, so far, they only have one link in this section.)
Chime on Macs
Resources for RasMol, Chime and other Molecular Visualization Programs
For Organic Chemistry: Submit a reaction for calculation (get animated xyz files)
Example Pages
A Model you can use for your first Chemscape Chime Web Page
Model 2: Adding Buttons to a Chime Model
Using buttons to display distances in Chime

Online Handouts to Get Started using RasMol and Chemscape Chime:
    Click here to either download or open a draft version of the objectives and goals for a RasMol and Chemscape Chime Workshop.
    Open or download the document called "RasMolreview.doc"
    How do I.doc is a one page summary of some of the features of both programs.

Dr. Cindy Klevickis
e-mail: klevicca@jmu.edu
office: CISAT Room 251
office phone: 568-2726
home: 298-8970

Buckminsterfullerene

RasMol is a stand alone application that can be used to create interactive images of molecules. RasMol was given free to the world to use and modify by its author, Roger Sayle (formerly from Glaxo Welcome.) Chemscape Chime (which is based on RasMol) is a plugin that allows users to embed interactive molecular visualizations, scripts and animation in web pages.

Links to Newer Versions of RasMol
The Open RasMol Home Page

RasTop
This version has a Windows Interface

If you don't see a rotating molecule in the left column, you need to download the Chemscape Chime Plugin

Link to the ISAT 454 Home Page

Getting Started with RasMol and Chemscape Chime

RasMol Lesson Plan for Water

water.pdb
water lattice.pdb
ice.pdb

Math Mol Lesson Plan for Water

Molecular Connections Case Example:
The Chemical Structures of Bowen's Series Crystals

PDB file links:

Olivine
Pyroxene
Amphibole
Biotite
Muscovite
alpha Quartz
beta Quartz

The molecular structure files for biotite and tremolite are from The Virtual Museum of Minerals and Molecules. These files were made available with permission of the Virtual Museum of Minerals and Molecules. Any redistribution of these files requires separate prior permission from their authors."

The olivine and muscovite pdb files are from Mineral Web by Alistair R. Lennie.

The pyroxine, amphibole, alpha quartz and beta quartz pdb coordinates are from Silica Polymorphs by Thomas Menard. (Note that, in this case, the pdb files can be edited to make atomic references easier in RasMol and Chemscape Chime.)

Links to other sites with crystal structure information

Mineral Web
The 3D Structure of Minerals
Crystal Lattice Structures:
Mineralogical Society of America
The Virtual Museum of Minerals and Molecules
Silica Polymorphs

What is a Bowen’s Series?

Find pdb files for each of the crystal structures.

Construct a web site to illustrate each step in the discontinuous series.

Include questions that students might answer by using your Bowen’s series tutorial.

Example questions:

Investigate each of the molecular structures and make a table of how the number of oxygen atoms shared by the silicate mineral changes through the reaction series?
Which minerals melt first?
Which minerals weather most easily?
Organize the silicate minerals in terms of how they might fit the following descriptions: isolated silicates, chain silicates, sheet silicates and framework silicates. How do the crystal structures of each of these silicate types relate to their physical properties?

Project Resources

Using Molecular Viewers on the Internet	This link died. If anyone finds it again please let me know. Cindy
More sites for pdb files for small molecules: Klotho (primarily biochemicals) NIH Molecular Modeling Page Small Molecule Database Cambridge Structural Database Small Molecules for Cell Biology Molecular Models for Chemistry(over 1250 molecular structure files) Chemistry Molecular Models from UW Stevens Point Many links to organic models PDB files for EPA Hazardous Chemicals	Great Chime Sites Surface Visualization with RasMol and Chemscape Chime The NCSA Chem Viz Page
The Protein Data Bank Image Library of Biological Macromolecules	More Examples of Student Projects
Chime Tutorials Amino Acids Glycolysis Interactive Biochemistry Molecules in Motion Web Elements Organic Chemicals Index Common Molecules Page	Enter a chemical formula and get a pdb file.

Molecular File Collections for RasMol Projects
For each collection, you will need a copy of
RasMol version 2.6 by Roger Sayle,
a copy of the RasMol help file and a set of moleclar structure (pdb) files.
Each set of files will fit on a single floppy disk along with the RasMol program and help files.

Earth Science, Geology, Materials Science and Other Physical Sciences	Life Sciences and Organic Chemistry
Household Chemicals
pdb file collection for "The Properties of Water"	Demonstration Assortment includes water, NaCl, DNA, alanine, caffeine, and p53 bound to DNA
pdb file collection for "The Geology of Silicates" The molecular "mol" and "xyz" structure files for albite, crystobalite jadite, and tremolite are available directly from from The Virtual Museum of Minerals and Molecules. Any redistribution of these files requires separate prior permission from their authors." The olivine and muscovite pdb files are from Mineral Web by Alistair R. Lennie. The pyroxine, amphibole, alpha quartz and beta quartz pdb coordinates are from Silica Polymorphs by Thomas Menard. (Note that, in this case, the pdb files may need to be edited to make atomic references easier in RasMol and Chemscape Chime.)	pdb file collection for Glycolysis and the TCA Cycle Many great sites already exist with Chime-based tutorials on glycolysis and the TCA cycle. Here are several links. There are many more. Do it Yourself Glycolysis
pdb file collection for "Environmental Air Quality"	pdb file collection for "Amino Acid Structures"
Some Molecules from Space A pdb file collection compiled by Bob Sandy	pdb file collection for "Nucleotides and Nucleic Acids"
pdb file collection for Carbon Crystal Structures graphite diamond Bucky balls helical tubes The helical structure is from Mauricio Terrones and Dr. Paul Birkett of the Sussex Fullerene Group, University of Sussex, for providing the helical structure. (c) Wyn Locke. 24 May, 1996, Link to http://origin.ch.ic.ac.uk/motm/	pdb file collection for "Lipids and Membrane Structures"
pdb file collection for "Making Steel" compiled by Fred Hoffman	pdb file collection for "Pharmaceutical Drugs"
pdb file collection for "The molecular story behind Karst Topography	pdb file collection for "Street Drugs" (This collection is open for "adoption.")
pdb file collection for "Materials Science"	pdb file collection for "Vitamins"
pdb file collection for "Atomic Orbitals" (This collection is open for "adoption.")	pdb file collection for "The Shapes of Organic Compounds" (This collection is open for "adoption.")
pdb file collection for The Top 10 Industrial Chemicals	We need lesson plans. Examples of possible projects include: "Learning about Environmental Science with Molecular Graphics" "Learning about Biology with Molecular Graphics" "Learning about Geology with Molecular Graphics" "Learning about Earth Science with Molecular Graphics" "Learning about Chemistry with Molecular Graphics" "Learning about the Properties of Materials with Molecular Graphics"
Shoebox Crystallography shoebox.pdb dude.pdb (Thanks to Carol Eglemann and her fine group.) plane.pdb (From Melynda Bailey and her tenacious group.) Rocket.pdb
Crystal Model Building Workshop NaCl unit cell (pdb) If the figure does not come up atomatically in Chime, choose "Ball and Stick from the Chime menu.) a=564 pm CsCl unit cell a=412 pm ZnS a=541 pm Quartz, SiO2 a=491; c=541 pm	I am writing a course outline for a 1 credit introductory science class this fall. The students will all be freshmen interested in K-6 teaching. If any of you have the time, inclination or interest to review what I have so far (Some parts are done; some are barely started.) You can read what I have here. Your comments will be greatly appreciated. ....... Cindy Here is the document: Science_discovery.doc

Funding is provided by the National Science Foundation