look out for CYSman!

Entering 

Molecular Heaven

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Most of these sites will require MDL's Chime™ plug-in, which works best with Netscape 4.7x -- NOT Netscape 6!!! [some of these sites absolutely require Netscape!] If you don't have these programs, see the downloads page first!

  

C4 Computers in Chemistry at Cabrillo College, CA        

http://c4.cabrillo.cc.ca.us        

a really excellent CHIME site, with tools and tutorials and a wide selection of molecules to view. Unfortunately, you can't get the site to work right with MS Internet Explorer™ even with the IE version of CHIME installed, so access it with Netscape Communicator™ 4.75 or 4.76. The C4 site was developed by Harry Ungar under a NSF grant and involved a host of students from Cabrillo and UC Santa Cruz  -- your tax dollars were VERY well spent on this one!

ChemViz Chemistry Visualization Program at NCSA, U. Illinois Urbana/Champaign

http://chemviz.ncsa.uiuc.edu/

with the Waltz interface to DISCO, CSD-Search interface, and ChemViz NanoCAD Interface

eChem Molecular Modeling Program from hi-ce*

*Center for Highly Interactive Computing in Education at the University of Michigan

http://hi-ce.org/sciencelaboratory/eChem/

"eChem is a simplified and learner-centered design version of professional visualizing tools. It allows students to build and manipulate three-dimensional models of molecules with a visualizer module. It also allows students to compare computationally predicted properties of the molecule with properties they observe in the laboratory. All views and modules are linked together, allowing the student to easily switch between various representations of the molecule."

I've tried it and it really is easy to use. Aimed at a high school audience, it has potential uses in higher ed as well. The lower picture at left shows L-cysteine in ball-and-stick (upper left), spacefill (lower left) and wireframe (both upper and lower right) displays. When the same molecule is shown in all four panels, they can all be simultaneously rotated.

Common Chemicals from the Reciprocal Net
formerly at  Indiana University Molecular Structures Center

http://www.reciprocalnet.org/common/index.html

check it out!

Molecular Viewing Gallery by A.C. Pratt at Dublin City University

http://www.dcu.ie/~chemist/pratt/JGallery/JGallery.htm

side-by-side Chime views of about 400 molecules listed alphabetically -- and it works with the IE version of Chime!

Molecular Modeling Center at NIH

http://cmm.info.nih.gov/modeling/

 

MDL Chime Site

http://www.mdli.com/chime/

links to many other sites featuring 3D Chime presentations of  molecules from those marvelous purveyors of Chime, the RasMol offspring that has revolutionized molecular visualization and made it available to all.

Molecules R US at NIH

http://molbio.info.nih.gov/cgi-bin/pdb

PDB search

Entrez  search and retrieval system from  NCBI   National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/Entrez/

Entrez is a retrieval system for searching several linked databases

featuring their  Cn3D  structure viewer 

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

Cn3D is something of an alternative to Chime -- with different capabilities; Cn3D can correlate structure and sequence information and reads .PNG files instead of .PDB files. It is very memory-intensive.

ExPASy (Expert Protein Analysis System) Molecular Biology Server of the Swiss Institute of Bioinformatics

http://us.expasy.org/

It's proteomic heaven!

HIC-Up
HIC-Up    Hetero-compound Information Centre - Uppsala

http://alpha2.bmc.uu.se/hicup/

a freely accessible resource for structural biologists who are dealing with hetero-compounds ("small molecules"); provided and maintained by Gerard Kleywegt at the Department of Cell and Molecular Biology, Uppsala University.
PDB files [VRML and Chime views] and lots of associated goodies!

Molecular Art/Molecular Science by David Goodsell at The Scripps Research Institute

http://www.scripps.edu/pub/goodsell/

lots of beautiful pictures from a master illustrator and links to articles containing them. Plan on spending some time here!

Molecular Modeling Representations by François Savary at U Geneva

http://scsg9.unige.ch/fln/eng/toc.html

the models aren't interactive, but they are nicely and concisely discussed. I liked this picture of ferrocene [or is it actually ruthenocene? -- it's eclipsed, not staggered] so much I used a smaller size as the molecular modeling icon in an earlier incarnation of this site.

Molecular Structure Center at U of Indiana

http://www.iumsc.indiana.edu/

Has the "Common Chemicals" page and lots more

Molecules.org at Lebanon Valley College

http://www.molecules.org/

lots of good stuff here -- check it out!

molecules alphabetically by W. F. "Flick" Coleman at Wellesley

http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html 

a very nice Chime site with hundreds of molecules indexed by central atom, formula, or name. Each individual picture has its own "control panel"  that has some of the normal Chime popup functions and some additional features like bond lengths and torsion angles. Works with both Netscape and IE versions of Chime!

molecules by Dave Woodcock at Okanagan University College, Kelowna, B.C., Canada

http://www.molecularmodels.ca/molecule/molecule_index.html
http://www.molecularmodels.ca/molecule/molecule.html
http://people.ouc.bc.ca/woodcock/molecule/molecule.html

A very nice Chime site with over 1400 molecules on file. The more I visit, the better I like it -- so much so that it's now one of my primary references for my CHEM 30B course. And bright-colored text on a black background, too -- what a great look!

molecules from NYU MathMol library

http://www.nyu.edu/pages/mathmol/library

GIF, VRML, and PDB files. You'll need Cosmo Player for the VRML and Chime/RasMol or WebLab for the PDB files.

Molecular Models for Biochemistry by William McClure at Carnegie Mellon University

http://www.bio.cmu.edu/Courses/BiochemMols/

Received uniform 5-star ratings from MERLOT peer reviewers on 7/22/01. This Chime-based site has excellent tutorials [some cleverly disguised as quizzes] on the use of Chime and RasMol, small molecules, protein architecture, glycolysis and the TCA cycle, and much more. A definite winner!  My IE 5.5 version of Chime 2.0 worked on this site, but a few micro-quasi-glitches or hesitations imply that Netscape 4.7x with Chime/Chimescape is probably more reliable.

Biomolecules at Kenyon College Molecular Biology Tutorials by BIOL 363 students and faculty

http://www2.kenyon.edu/depts/biology/BMB/chime.htm

Really excellent Chime-based tutorials that work with Chime 2.6 SP4
in either MS IE 5.5/6.0 or Netscape 4.7x [and, I've been told, Netscape 7]
Previous plugin problems have been fixed!

IMB Image Library of Biological Macromolecules  by Institute for Molecular Biology, Jena

http://www.imb-jena.de/IMAGE.html

a really extensive database; when you select an entry, a page with a GIF picture like the one shown comes up; you can then usually choose to view the molecule with RasMol or Chime

Inorganic Structure Database by Scot Wherland at Washington State U

http://www.wsu.edu/~wherland/wwwlist03.htm

Viewable with Chime, RasMol [Berkeley version] or WebLab Viewer; 330 structures available including the Fe(III) oxalate complex at left.
more great inorganic resources are at
http://www.wsu.edu/~wherland/

Klotho : Biochemical Compounds Declarative Database

http://www.ibc.wustl.edu/moirai/klotho/compound_list.html

static GIF pictures and Chime/Rasmol viewable pictures of several hundred biomolecules. really heavy on nucleotides

molecules  by  Paul Schueler at Raritan Valley CC, NJ  

http://www.raritanval.edu/departments/Science/molecules.html

neat CHIME stuff with a small but well-selected collection of molecules; I've been using this site extensively in my own teaching until I get my own put together

Molecular Origami by Bob Hanson and Ben Murray at St. Olaf College

http://www.stolaf.edu/people/hansonr/mo/

a program that enables you to pick and choose from a RasMol display only those portions of a molecule that you are interested in.

Folding@home: From Genome to Structure by Vijay Pande at Stanford U

http://www.stanford.edu/group/pandegroup/Cosm/

you can download software and get involved in solving some problems, but there is also a lot of useful background related to protein folding.

 

Mol4D  Molecules in Four Dimensions by CMBI Center for Molecular and Biomolecular Informatics at U Nijmegen, het Nederlands  

http://www.cmbi.kun.nl/wetche/organic/

lots of good stuff here -- really good tutorials and more

 

3D Molecules by Vagelis Baboukas at ECPL, U of Crete 

http://ecpl.chemistry.uch.gr/~baboukas/Java/3Dmol/General.htm

In English or Greek!  Chime-like pix, but the manipulation menu is different and takes some getting used to...

Molecular Science Project at UCLA

http://www.molsci.ucla.edu/

tutorials and an interesting "calibrated" peer-review student writing center. You need Netscape for best results, and even then, many links seemed to be broken the last time I checked (10/15/01)

Molecular Structure Pages at Purdue University

http://www.chem.purdue.edu/gchelp/molecules/index.html

Chime structures of ~500 molecules and complex ions listed by formula

Online Macromolecular Museum at California Lutheran University

http://www.clunet.edu/BioDev/omm/gallery.htm

works best with the Netscape version of Chime, although I was able to access a large part of the site with the IE version. Beautifully-done tutorials on about 30 topics of particular interest to cell and molecular biologists.

PDB  Protein Data Bank from RCSB Research Collaboratory for Structural Bioinformatics  and Mirror Sites

http://www.rcsb.org/pdb/     San Diego Supercomputer Center

http://rutgers.rcsb.org/pdb/   Rutgers U

http://nist.rcsb.org/pdb/      NIST

http://pdb.ccdc.cam.ac.uk/pdb/    Cambridge U

http://pdb.bic.nus.edu.sg/pdb/   National U of Singapore

http://pdb.protein.osaka-u.ac.jp/pdb/    Osaka U

http://www.pdb.ufmg.br/pdb/    U Federal de Minas Gerais, Brazil

  need viewer like RasMol or CHIME to view .pdb files. They also have a "molecule of the month" section with nonmanipulable images like those at left



PDB Chime Structures by Robert J. Lancashire at the University of the West Indies, Mona, JA

http://wwwchem.uwimona.edu.jm/spectra/PDBfirst.html

Use Netscape!  A nice selection of 40+ inorganic and 90+ organic compounds, including the notorious hypoglycin, seen at left, from the ackee fruit.

The remainder of the UWI chemistry site is also well worth exploring.

http://wwwchem.uwimona.edu.jm/uwichem.html

Dr. Lancashire's home page is at

http://wwwchem.uwimona.edu.jm/chrl.html

see more on my "spectral city" page

SCOP  Structural Classification of Proteins 
by Alexey G. Murzin, Loredana Lo Conte, Bartlett G. Ailey, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia at the Medical Research Council, Laboratory of Molecular Biology, Cambridge University

http://scop.mrc-lmb.cam.ac.uk/scop/index.html

Structures of proteins grouped by families, viewable with Chime and other viewing programs

Proteins: Interactive Biochemistry Pages at U Virginia

http://cti.itc.virginia.edu/~cmg/Demo/molecule.html

Yessss! Interactive Chime tutorials that really work!!!

Uppsala University Electron Density Server

http://fsrv1.bmc.uu.se/eds/

GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A Wählby & TA Jones (2003).
"The Uppsala Electron Density Server (EDS) - a touch of reality". To be submitted.
Javascript viewing of PDB files from a searchable database. Ramachandran plots and much more....

Virtual Model Kit from Western Washington University

http://atom.chem.wwu.edu/dept/vmolckit/molecule.html

selected Chime structures particularly geared for undergrad organic

Water Structure and Behavior by Martin Chaplin at South Bank U  

http://www.sbu.ac.uk/water/

This site provides an excellent and extensive background on the physical and chemical characteristics of the quintessential elixir. Has COW and Chime depictions of many molecular arrangements. For a different perspective, you might also want to check out Steve Lower's AquaScams site in the pseudoscience section.

WebMol JAVA PDB Viewer developed by Dirk Walther at UCSF 

http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl

download from  http://www.cmpharm.ucsf.edu/~walther/webmol/download.html

API version at    http://www.cmpharm.ucsf.edu/~walther/webmol/

and mirrored at the European Molecular Biology Laboratory at Heidelberg

http://www.embl-heidelberg.de/cgi/viewer.pl/

A feature-rich, tool-equipped alternative to Chime/Rasmol for viewing PDB structure files. Can be run as an applet or as a stand-alone application.

World Index of Molecular Visualization Resources by Eric Martz and Trevor Kramer; server courtesy Philip Bourne and San Diego Supercomputer Center

http://molvis.sdsc.edu/visres/

As Brigham Young said, "This is the place!" 

As Eric Martz says, "USE NETSCAPE!" for Chime stuff

As Ron says: NOT the dreaded Netscape 6!!!

You can't go wrong at this site, which lists scores of Chime sites, organized in several different ways. Be ready to spend hours here!

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Last update  1 / 24 / 06