Gale Rhodes

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Crystallography Made Crystal Clear, signed by author, at, from this merchant: 15 Beacon Ink
• 3rd Edition, new and used, sold out.
2nd Edition NEW
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For brief descriptions of resources, browse this page.

DeepView Tutorial

Bioinformatics Tutorial

Stereo Viewing Tutorial

Judging Model Quality:
A Glossary

Pet Peeve Style Manual

Student-Led Discussion Manual

Little Library for the Reading-Time Challenged

Home Page for Crystallography Made Crystal Clear

Resources for Biochemistry Teachers

Molecular Graphics

Teach yourself how to see and analyze macromolecular structure.

Tutorial for DeepView
UPDATED for v. 4.0.

From first steps to advanced use of a free, friendly, and powerful molecular graphics program.


Bioinformatics for Beginners
UPDATED 2008/10. How to use sequence and structure databases. Designed for newcomers, including first-year biochemistry students. INCLUDES HOMOLOGY MODELS -- using sequence and homologous structures to model proteins of unknown structure.

Judging the Quality of Macromolecular Models

Glossary of Terms to help you understand journal articles, and to make wise use of structures determined by X-ray crystallography, NMR, and homology modeling.

Stereo Viewing

See Models in 3D
See what everyone else misses about structure by viewing in 3D.

New Life for Seminars and Journal Clubs

User's Manual for Student-Led Discussion
Improve and increase student participation—more informed talk from students, more thoughtful listening for you.

Improve Your Writing

The Pet Peeve Style Manual
Eliminate annoying and confusing words and phrases from your scientific writing. Your readers will thank you.

Refreshment for Your Mind

Little Library for the Reading-Time Challenged
You can't think about structural biology all the time. Make the most of outside reading and broaden your education with these small but pithy books. All worth reading and rereading.


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Welcome to

The Molecular Level

Tools for Structural Biology
Education and Training

Can Your Molecular Modeling Program Do This?
A Deep View of DeepView Version 4.0

Back Cove & Opsin

Simplicity: Photons and Protons
Composite image, Back Cove (Portland, Maine) and model of bacteriorhodopsin

During daylight hours, proteins like this one are hard at work for certain types of photosynthetic bacteria in the Cove's surface waters. Bacteriorhodopsins of archaebacteria and their recently discovered marine bacterial relatives, proteorhodopsins, transform light energy into chemical energy, using absorbed light (photons) to pump hydrogen ions (protons) across cell membranes. The resulting disparity between the quantities of protons inside and outside the bacterial membrane, called a concentration gradient, is a fundamental and versatile source of chemical energy that bacteria use for maintenence, propulsion, and reproduction. Bacteria are important links in food chains that support the abundant and varied life of Back Cove.

By using photons to pump protons, photosynthetic rhodopsins forge a link between two of the universe's simplest entities.

Image ©2001 Gale Rhodes
(prepared with DeepView and Canvas)

Foundations of
Structural Biology

I was captured for life
by chemistry and by crystals.

Dorothy Hodgkin

Made Crystal Clear:
A Guide for Users of Macromolecular Models

by Gale Rhodes
Third Edition, 2006

Elsevier/Academic Press

CMCC Covers

CMCC-III covers the basics of single-crystal X-ray crystallography for users of macromolecular models and beginning crystallographers. Includes brief introductions to NMR and homology models, and to other diffraction methods (electron, neutron, Laue, fiber, and powder).
Learn where all types of models come from and how to use them wisely.

Learn more about CMCC-III .

Visit the CMCC Home Page.
Links to all tools mentioned in the book, plus sites that expand your understanding of macromolecular models.

Biochemistry Resources

Without biochemistry, you miss most of the beauty in structural biology. Learn or review key concepts with these tools. Student-tested and compatible with standard texts.

Biochemistry Topics List
Integrated with all of the following Biochemistry Resources.

Biochemistry, Chapter Zero: Setting the Stage for Biochemistry
Get acquainted with metabolism while reviewing essential concepts from general and organic chemistry.

Learning Strategies
Get a foothold on new subjects.

Essential Skills
Ready to move to the next topic?

Learning Biochemistry with DeepView
Problems and tutorials that require molecular graphics, and DeepView does them best.

A grab-bag of learning aids for beginning biochemistry.

O-CHem Directory
Review your organic chemistry. Prepared by Professor Thomas Newton.

Molecular Graphics Manifesto
Molecular graphics should be an integral part of a first biochemistry course. Here's why.

Biochemistry Resources
Links to all of the above and more.

Disclaimer: Statements at this site represent the views of Gale Rhodes, and not of any other organizations associated with these pages. Links to other pages do not constitute endorsement of products or services. The author receives no compensation for links on this site. Take precautions with any online seller to protect your personal and financial information. If it's cold out, wear a warm coat.