Welcome to the CMCC Home Page

See Author's Book Sale, Below

Covers of Three Editions

Resources for Readers of

Crystallography Made Crystal Clear

A Guide for Users of Macromolecular Models

Third Edition, February 2006, Elsevier/Academic Press

Gale Rhodes
Contact Information

Crystallography Made Crystal Clear,
signed by author,
at Amazon.com, from this merchant: 15 Beacon Ink
3rd Edition NEW
3rd Edition USED
2nd Edition NEW
Supplies are limited.


Reviews of Earlier Editions

ORDER THIS BOOK: Amazon // Barnes and Noble // Borders

(9 Mb zip archive)

Click for a A Very Brief Introduction to Protein Crystallography

CMCC Home page contains links to all web resources referred to in the third edition (2006) of CMCC. In addition, this page provides up-to-date links to selected other web sites that might of interest to to CMCC readers.

I do not intend to make CMCC Home Page an exhaustive source for crystallographers or structural biologists. My emphasis is on sites that can help CMCC readers, or those with similar experience, to take the next steps in expanding their knowledge of macromolecular structure determination, modeling, and prudent use of models.

Links to outside pages open in a NEW BROWSER WINDOW. To return to this page, close the new window. To go to the table of contents from anywhere on the page, click on the nearest peptide chain, like this one:

link to table of contentns

Do you know about the Grameen Foundation?



Looking for a web site mentioned in CMCC-3?

Web sites and servers mentioned in the book are listed under the chapter of their first mention.

Chapter 1. Model and Molecule
DeepView (aka Swiss-PdbViewer) Home Page
POV-Ray Home Page

Chapter 2. An Overview of Protein Crystallography
Book of Fourier, by Kevin Cowtan

Chapter 3. Protein Crystals
Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth

Chapter 4. Collecting Diffraction Data
Synchrotron Radiation Sources Worldwide
List maintained by ESRF, the European Synchrotron Radiation Facility

Chapter 5. From Diffraction Data to Electron Density
Interactive Structure-Factor Tutorial, by Kevin Cowtan

Chapter 6. Obtaining Phases

Chapter 7. Obtaining and Judging the Molecular Model
Bayesian Inference: Calculation for simple of example of likelihoods, CMCC-3, p. 165.
Protein Data Bank

Chapter 8. A User's Guide to Crystallographic Models
Judging the Quality of Macromolecular Models, a Glossary of Terms from CMCC
EDS, Electron Density Map Server at Uppsala
Model Validation
, by Gerard Kleywegt
MolProbity, by Jane and David Richardson
RNABase, the RNA Structure Database, with special tools for judging RNA model quality.

Chapter 9. Other Diffraction Methods
IIMS, Electron Microscopy Database at European Bioinformatics Institute (database appears to be under development)

Chapter 10. Other Kinds of Macromolecular Models
ExPASy, Expert Protein Analysis System
Swiss-Model, Homology Modeling Server
Other Homology Modeling Servers (list)
Specialized Homology Modeling Servers
-- Unable to find any as of 2006/01/06
G-Protein Coupled Receptors
-- See Swiss-Model in GPCR Mode
-- Also see "Other sites related to 7TM/GPCR proteins" at the bottom of the GPCR-mode page at Swiss-Model.
-- See Swiss-Model in Oligomer Mode
Databases of Theoretical Models
Swiss-Model Repository (a data base of automatically produced homology models)
Other Databases of Homology Models, list at Emory University
Databases of Other Theoretical Models

Chapter 11. Tools for Studying Macromolecules
Stereo Viewing, How to See in 3D
Molecular Graphics Programs
DeepView (aka Swiss-PdbViewer), my personal favorite, for beginners and researchers alike. OS X version is incomplete. Mac users should stick to the OS 9 or Classic version for now.
RasMol, the first really powerful viewer that ordinary mortals could use, still widely used. Scriptable for making movies or interactive tutorials. A plug-in version called Chime is widely used to insert interactive viewing windows (with extensive pop-up menus) into web pages. Chime's support is declining (never coming to OS X), and many writers of such pages are switching to JMol, next.
JMol, Java applets in standalone and plug-in versions that are similar to RasMol and Chime. Developers goal is for these programs to run RasMol and Chime scripts unaltered. The standalone version is a pretty friendly little first viewer. Protein Data Bank provides a JMol viewer. Right-click the graphics screen to see pop-up menus.
Protein Glimpse, a Mac OS X Widget, similar to using the JMol Viewer at Protein Data Bank. Uses JMol.
Protein Explorer, browser-based viewer that uses Chime, a plug-in version of RasMol. Windows or Mac OS-9 only. Coming eventually in Jmol version.
KiNG (Kinemage, next generation), a Java application for viewing kinemages and text windows to describe them.
Protein Data Bank allows you to uses several molecule viewers. Here are two approaches:
-- Click on Software Tools, and then Molecular Viewers Help, for information about some of the friendliest and most stable molecular graphics programs.
-- OR, search for a model (try 1BL8), then click Display Molecule, and try the viewers listed there.
Molecular Visualization Resources, by Eric Martz, provides information on, and access to, just about every known tool in the universe for viewing and studying molecular structure.
Tutorials for Molecular Graphics Programs
DeepView (Swiss-PdbViewer)
For more, see Molecular Visualization Resources.
Atomic Coordinate File Conversion
Dundee PRODRG2 Server
ChemAxon's Marvin Applets
Docking Tools and Servers
List maintained at Boston University
List maintained at Emory University
Cold Spring Harbor Laboratory (see Courses and Meetings)

Want to learn more about structure determination?

Web sites listed here are good places to expand your understanding beyond the level of CMCC-3.

  1. Why Does CMCC Begin With a Poem?

  2. More About CMCC Itself: Preface and Reviews, First and Second Editions

  3. A CMCC Glossary: Judging the Quality of Macromolecular Models

  4. More on Crystallographic Model Quality

  5. Tutorials in Computer Graphics

  6. Join world-wide discussion of Swiss-PdbViewer users!

  7. Stereo Viewing

  8. Data Banks of Macromolecular Models

  9. Data Bank of Electron-Density Maps

  10. More About Crystallography

  11. More About Crystals

  12. More About Synchrotron Radiation Sources

  13. Detailed Look at a Synchrotron Radiation Source (CHESS)

  14. More About the Fourier Transform and Structure Factors

  15. More About NMR

  16. More About Homology Modeling

  17. ExPASy: Tools for Structural Biologists

  18. Please Suggest Other Links !

  19. SEE AND REPORT CORRECTIONS TO CMCC-III HERE. (none yet, fingers crossed)

  20. See and report corrections to older editions here.

  21. Feedback: How do you use CMCC?

Link to Table of Contents

Why Does CMCC-II Begin With A Poem?

Thanks to A. R. Ammons (1926-2001) and his publishers for allowing me to grace my book with his poem, "Phase". This poem contains images that remind me of things crystallographic, and it also includes some common terms, such as phase, that have various meanings in the English language, but quite specific meaning in crystallography. I used Ammons's images as analogies in several places in the book, and I drew contrasts between common and crystallographic meanings of terms. Can you find my allusions to the poem?

If you enjoy this poem, you might want to learn more, or even more, about A.R. Ammons.

Judging Model Quality

CMCC did not have a glossary, but it does now -- one with a special purpose. This illustrated glossary confines itself to terms that are crucial to judging the quality of macromolecular models from crystallography, NMR, and homology modeling. If you don't know or can't remember the meaning of temperature factor, restraint, or threading energy, then this is the page for you.

More on Crystal Model Quality

Model Validation, Tutorial by Gerhard Kleywegt, Uppsala University

An extensive and informative tutorial that will turn you into an astute judge of model quality. Be the first kid on your block to really know whether you are working with a good model.

MolProbity: Powerful Browser-Based Model Validation Tools

Another great site for learning about -- and doing -- model validation. This site provides all the tools you need in the form of Java applets, including the latest versions of Kinemage software, either the stand-alone program Mage, or the applet KiNG. The tools at this site can grab PDB files, electron-density maps, and other resources as you work. Includes step-by-step guidance for beginners.

Real Ramachandran Plots, by Sven Hovmoeller, Stockholm University

As a tool for use in predicting protein folding, Professor Hovmoeller has compiled Ramachandran diagrams showing the actual range of phi and psi values for each of the common amino acids, as they occur in all proteins in the Protein Data Bank. These diagrams are informative, useful, and pretty as well. At Professor Hovmoeller's home page, click on Projects, and then on Protein Folding Prediction and Ramachandran Plots.

RNABase, the RNA Structure Database

Special tools for judging RNA model quality, as part of a database of all RNA structures. Links to PDB entries of RNA structures and protein-RNA complexes. Judging model quality for nucleic acids is a whole new ballgame; get your first batting and fielding practice here.

Computer Graphics Tutorials for Swiss-PdbViewer and RasMol

The following tutorials are designed for beginners in macromolecular modeling. They are especially appropriate for beginning biochemistry students at the time they are learning about protein structure (after the first 5 or 6 weeks of the first semester course). The tutorials teach both the use of a computer program and basic principles of protein structure. They also introduce the Protein Data Bank. Both tutorials have been used and tested by many teachers, students, and researchers.

Tutorial for Swiss-PdbViewer (Deep View)

Learn how to use Swiss-PdbViewer by working through a self-guiding introductory tutorial. Start with simple viewing, but if you wish, go on to sophisticated comparison and analysis of structures, judging the quality of models, and homology modeling. No previous experience with molecular graphics required. You'll be a skillful modeler by the time you finish this tutorial. For version 3.1.

Swiss-PdbViewer Home

Get the free program Swiss-PdbViewer, a powerful tool for macromolecular viewing, structural analysis, comparison of models, and model building.

Tutorial for RasMol

Learn how to use this popular macromolecular viewing tool by working through a self-guiding introductory tutorial. No previous experience with molecular graphics required. For version 2.6b2.

RasMol Home

Get the free macromolecular viewer RasMol, as well as many resources for teaching structural biology using RasMol and its plug-in version Chime.

Link to Table of Contents

Stereo Viewing

Learn how to see the 3-D in stereo pairs while using computer graphics, reading journals, and even on projection screens during classes or seminars -- without special viewers. Good eye-muscle exercise as well.

Link to Table of Contents

Data Banks of Macromolecular Models

Protein Data Bank

Get models to view on your computer. The Protein Data Bank (PDB) is the world's most complete source of macromolecular models obtained by the experimental methods of diffraction and NMR. Models are provided as files of atomic coordinates in just the format you need for viewing with Swiss-PdbViewer or other graphics programs. In addition, PDB files are linked to MedLine abstracts of the papers that describe the structures.

SWISS-MODEL Repository

Currently a repository for macromolecular models obtained by automated homology modeling. This or a similar site will eventually become the PDB-like repository for all theoretical (non-crystallographic / non-NMR) models.

Link to Table of Contents

Data Bank of Electron-Density Maps

Enter a PDB file code and download an electron-density map. You can view maps with Swiss-PdbViewer and other graphics programs to see the quality of the map on which the structure is based. If there is no map available for your PDB file, there are two possible reasons: 1) the crystallgraphers did not deposit the x-ray data (structure factors) at the Protein Data Bank, or 2) the file is too new -- just wait awhile.

Link to Table of Contents

Crystallography 101

Good next step after CMCC for learning more about macromolecular crystallography. This complete short course in x-ray crystallography features excellent illustrations, interactive images, and problem solving.

Link to Table of Contents

A Practical Guide to Protein Crystallization

How to grow and screen crystals for X-ray Crystallography. Be sure to look at the bottom of the page for links to beautiful pictures of protein crystals.

Link to Table of Contents

BioSync A Resource for Synchrotron Radiation Users

This web site, maintained by the San Diego Supercomputer Center, is intended to provide technical, administrative, and logistical information to prospective synchrotron users in the field of macromolecular crystallography. The site is being developed on behalf of the Structural Biology Synchrotron Users Organization(BioSync). BioSync was formed in 1990 to promote access to synchrotron radiation for scientists whose primary research is in the field of structural biology.

Link to Table of Contents

Nuts and Bolts of Synchrotron X-ray Sources

Home pages for the worlds sources of high-energy X-rays for crystallography. Most sites include a virtual tour.

Link to Table of Contents

Kevin Cowtan's Book of Fourier

Highly informative and revealing graphical illustrations of the Fourier transform and its application to structure determination by diffraction methods. Thanks to Kevin Cowtan for allowing me to use some of his excellent images in CMCC. Many additional vivid illustrations at this site.

Link to Table of Contents

The Basics of NMR

Thorough introduction to NMR theory. Brief treatment of two-dimensional NMR near the end.

2D NMR Spectroscopy

Introduction to the principles of two-dimensional NMR. Emphasis on small molecules, but you need to understand these principles before pursuing a deeper understanding of multidimensional, macromolecular NMR.

Practical Applications of NMR Spectroscopy in Biochemistry

Big molecules at last! Syllabus for Professor Gordon Rule's course, Structural Biophysics 03-871, at Carnegie Mellon University. Nicely illustrated lecture outlines for most of the course topics.


A repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids.

Link to Table of Contents

Principles of Protein Structure, Comparative Protein Modeling, and Visualisation

by Nicolas Guex and Manuel C. Peitsch

Excellent illustrated introduction to the methods and limitations of homology modeling, starting with the basics of protein structure.

Link to Table of Contents

ExPASy (Expert Protein Analysis System)

Powerful suite of computer tools and data bases for molecular biologists. ExPASy is the molecular biology WWW server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as identification of proteins by 2-dimensional polyacrylamide gel electrophoresis. Swiss-PdbViewer is especially designed to work with ExPASy structure tools.

Link to Table of Contents

Please Suggest Other Links!

If you find a web resource that you think I should list here, or if you want your own site linked to this page, please send me the URL and I will take a look. Remember that the modest goal of this page is to help CMCC readers, as well as others of similar experience, to take their next steps in learning more about macromolecular structure, structure determination, modeling, and wise use of models. See bottom of page for my email address.

Link to Table of Contents

Correcting Errors in CMCC-II

No book is perfect. If you find an error of any kind in CMCC-II, please notify me. I want to know about typographical errors, errors in figures, conceptual errors, even misleading or unclear passages. Your help can eliminate minor errors in future printings.

At this site, I will provide corrections for all errors, including repaired figures that you can download and paste into your copy. For error notices received to date, click the heading of this section.

Correcting Errors in CMCC-III

Appearing soon.

Link to Table of Contents

How Do You Use CMCC?

I will appreciate feedback about how you have used CMCC, either edition, in your research, teaching, or personal learning. Such feedback my help me to make the book and this page more useful to more readers.


Protein Stereo Model


Model and portion of electron-density map of bovine Rieske iron-sulfur protein (Protein Data Bank code 1rie). The electron-density map is contoured only around selected residues and the iron-sulfur center. For discussion, see Figure 11.9 and Chapter 11 of CMCC-III.

Image prepared using Swiss-PdbViewer and POV-Ray. This stereo pair is designed for convergent (cross-eye) viewing.

About Protein Crystallography

"I was captured for life by chemistry and by crystals."
Dorothy Hodgkin

Just as we see objects around us by interpreting the light reflected from them, x-ray crystallographers "see" molecules by interpreting x-rays diffracted from them. Molecules are too small to diffract visible light, but x-rays are of shorter wavelength, and thus can illuminate molecules. Each molecule diffracts too weakly to be seen, but when many molecules are aligned in a crystal, all diffracting in unison, diffracted rays are strong enough to detect and interpret. That's why protein crystals are essential to learning protein structure.

The actual molecular image obtained from crystallography is called an electron-density map (represented as a red net above, and also in this more detailed image). The crystallographer then interprets the image by building a model (balls and sticks in the figure above), fitting the known chemical contents of the protein into the map. This entails displaying map and model on a computer and fitting the model to the map. Often, the crystallographer represents frequently occuring structural elements of proteins as cartoons, like the blue and red ribbons, which are shorthands for beta sheets (blue) and alpha helices (red) of proteins. So as you look from top to bottom, the figure becomes more interpretive: first the raw image (net), then the atomic interpretation of the image (balls and sticks), and finally, cartoons (ribbons) that are shorthand for common structural elements of proteins.

To Top of Page

Link to Table of Contents

Peptide page-divider image prepared with DeepView (aka Swiss-PdbViewer).

Gale Rhodes
Contact Information

TO The Molecular Level

Visitors Since February 2006 (release of CMCC-III)  


Visitors Since January 2000 (release of CMCC-II)