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Grameen Foundation?
Its founder, Muhammad Yunus, and the Grameen Bank won the
2006 Nobel Peace Prize.

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Student resources at my
USM Home Page.

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Tools for Structural Biologists

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Graphics Tutorials

Teach yourself how to see and analyze macromolecular structure with computer graphics programs.

Tutorial for Deep View
(also called Swiss-PdbViewer)
From first steps to advanced use of a friendly but powerful tool for structure research.

Tutorial for RasMol
The basics of an aging, but still widely used tool for teaching molecular structure. Might also help you with JMol, which has similar command structure.

Bioinformatics Tutorials

Bioinformatics for Beginners
Using sequence and structure databases, Designed for biochemistry students and other newcomers. INCLUDES INTRODUCTION TO HOMOLOGY MODELING -- using sequence and homologous structures to model proteins or unknown structure.

Judging the Quality of Macromolecular Models

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

Stereo Viewing

See Models in 3D
Enhance your ability to see your way around withing macromolecules by viewing in 3D.

New Life for Seminars and Journal Clubs

User's Manual for Student-Led Discussion
Put prepared students in the driver's seat in seminar courses. Improve and increase student participation -- more talk from students, more listening for 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.

Sponsors

Establishment of
The Molecular Level
was made possible by a generous gift to the USM Annual Fund in memory of late Professor Emeritus of Chemistry Alan Smith. Additional support has come from these sponsors:


Apple Computer

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The University
of
Southern Maine

www.usm.maine.edu

with special considerations from

PaveAmericaProject

 

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TEACHERS may use these tools freely in their courses.
See Agreement for Use.

Did you take biochemistry courses with me?
Click HERE.

Welcome to

The Molecular Level

Tools for Structural Biology Education and Training

Gale Rhodes, Professor Emeritus of Chemistry
University of Southern Maine
Contact Information

This site featured in Netwatch, Science, and Internet Scout Project.

Crystallography Made Crystal Clear
3rd Edition. Click HERE.

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)

Biochemistry Resources

Command of biochemistry is crucial to developing molecular-level understanding in structural biology. Use these tools to learn or review key biochemical concepts and skills. Compatible with any current biochemistry text.

Learning Tools for Biochemistry Courses

NEW! Biochemistry, Chapter Zero: Setting the Stage for Biochemistry
A review of essential concepts from general and organic chemistry. This review provides a metabolic context for organizing your study of biochemistry. Added 2006/09/19.

Learning Strategies
Getting a foothold on new subjects.

Essential Skills
Don't show up for an exam without these skills.

Supplemental Problems
You can solve these problems ONLY with molecular graphics!

Biochemistry Topics List
For a one-year course, integrated with all of the Biochemistry Resources.

Reviewing Organic Chemistry
Need to review an O-chem topic for your biochemistry course? Go to the excellent O-CHem Directory, prepared by Professor Thomas Newton.

The Well-Read Biochemist:
A Scientist Encounters the Humanities
Poems, essays, fiction, and art -- through the eyes of a structural biologist.

Small Song

The weeds give
way to the

wind and give
the wind away

A. R. Ammons

A Graphics Manifesto

If you are not training your first-year biochemistry students to use molecular graphics and the Protein Data Bank as tools for independently exploring macromolecular structure, YOU ARE FAILING THEM IN AN IMPORTANT AREA. To see why, read my Molecular Graphics Manifesto.

 

 

Foundations of
Structural Biology

Crystallography
Made Crystal Clear:
A Guide for Users of Macromolecular Models
by Gale Rhodes
Third Edition, 2006
Elsevier/Academic Press

CMCC Covers

Basics of single-crystal X-ray crystallography, for beginning crystallographers and users of macromolecular models. Includes brief introductions to NMR and homology models, and to other diffraction methods (electron, neutron, Laue, fiber, and powder).

Learn more about this book.

and an integral part of
Crystallography Made Crystal Clear:

CMCC Home Page
Support for readers of my book, including links to sites that further expand your understanding of crystallography and crystallographic models.

 

World's Smallest
Style Manual

Always Under Construction
Send me your favorite unfavorites.

Improve your writing. Search your documents and eliminate all instances of these words and phrases:

=> at this point in time -- many needless words.
What's wrong with now?
=> concomitant -- vague word implying accompaniment, but things can accompany each other in many ways. Pick the word that describes the situation precisely: associated, connected, consequent, related, resultant.
=> copious quantities -- old chemistry jargon.
Try plenty.
=> due to the fact that -- more needless words.
Use because.
=> in close proximity -- redundant and unnecessarily complex. Ever heard of distant proximity?
Use near.
=> instantiate -- philosophical and education jargon, meaning "to be an instance (or example) of.. ." Made by turning the nice little word "instance" into an ugly verb. I call this atrocious act "verbing", an ugly word that is an example of itself.
=> instantiation -- an instance. Made by turning the ugly verb "instantiate" (see above) into an even uglier noun. But we already have a noun; we made the ugly verb from it. Use the noun.
Use instance.
For a hilarious example of horrid writing (and not very clear thinking, either) featuring the instantiate family of words, see Science 25 April 2008:
Vol. 320. no. 5875, pp. 454 - 455, LEARNING THEORY:
The Advantage of Abstract Examples in Learning Math. (Imagine people who talk like this trying to tell people how to teach.)
=> orientate -- one extra syllable turns a lovely word into something grating.
Use orient.
=> problematic -- vague jargon.
Pick the word that describes the problem precisely: arduous, arguable, challenging, complex, confusing, debatable, difficult, disputed, hard, knotty, moot, puzzling.
=> utilize -- one of the language's ugliest words. The word means use.
Use use.
=> more to come...

Disclaimer: Statements at this site represent the views of Gale Rhodes, not those of the University of Southern Maine or its Chemistry Department. 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.