01 / Reading Guide
Reading Guide
Citation
Müller, P., Herbst-Irmer, R., Spek, A. L., Schneider, T. R., & Sawaya, M. R. (2006). Crystal Structure Refinement: A Crystallographer's Guide to SHELXL. Oxford University Press (International Union of Crystallography Texts on Crystallography).
Chapter Summary
The book is a mixture of textbook and tutorial. Its subtitle names its focus, the refinement program SHELXL, and the back-cover description states that it covers advanced aspects of practical refinement that earlier textbooks had not much addressed. Most chapters give refinement examples based on SHELXL and describe each problem in detail, and a CD-ROM supplies the files needed to reproduce the refinements. Peter Müller wrote most chapters; Regine Herbst-Irmer, Anthony Spek, Thomas Schneider and Michael Sawaya contributed the chapters noted below. A foreword opens the volume.
Chapter 1: SHELXL
An introduction to the program: the SHELX suite, how SHELXL is organized, and its input files.
Chapter 2: Crystal structure refinement
A brief survey of refinement as a whole. It treats least-squares refinement, weak data and resolution cut-offs, residual factors, the parameters of a model, and the use of constraints and restraints.
Chapter 3: Hydrogen atoms
Hydrogen atoms are hard to locate in X-ray structures. The chapter explains that hydrogen atoms bound to carbon can usually be placed by calculation, whereas acidic N–H or O–H hydrogens should be found in the experimental electron density.
Chapter 4: Atom type assignment
How to decide which element each electron-density peak represents, using crystallographic and chemical knowledge such as displacement parameters, bond lengths and coordination geometry.
Chapter 5: Disorder
Covers static and dynamic positional disorder, substitutional disorder and bulk solvent, and how to describe them in SHELXL using constraints, restraints and free variables.
Chapter 6: Pseudo-Symmetry
Treats pseudo-symmetry, the topic that follows disorder and precedes twinning in the book's sequence of harder refinement problems.
Chapter 7: Twinning
Written by Regine Herbst-Irmer. The chapter defines four types of crystallographic twinning, shows how twin laws are derived, and includes six worked SHELXL refinement examples.
Chapter 8: Artefacts
Examples include shortened bond lengths caused by libration and inaccurately determined hydrogen positions, together with a warning against using "artefact" as an excuse for careless work.
Chapter 9: Structure validation
Written by Anthony L. Spek. A short chapter on validating small-molecule structures.
Chapters 10–11: Protein refinement; Protein structure (cross) validation
Thomas R. Schneider writes the single chapter on the refinement of macromolecular structures, and Michael R. Sawaya the second short validation chapter, on proteins.
General remarks
The volume ends with a section of general remarks by Müller.
Key Concepts
Chapters 1–4: Foundations of refinement
- Least-squares refinement: adjusting model parameters to fit the diffraction data.
- Constraints and restraints: ways to impose chemical knowledge on a model, such as geometric restraints.
- Hydrogen atom treatment: calculated versus experimentally located positions.
- Atom type assignment: deciding which element an electron-density peak represents.
Chapters 5–8: Difficult cases
- Disorder: static, dynamic and substitutional disorder, and bulk solvent.
- Pseudo-symmetry and twinning: twin laws and their use in refinement.
- Artefacts: apparent features that arise from the data or the model rather than the molecule.
Chapters 9–11: Validation and proteins
- Structure validation: checking a refined model for errors and inconsistencies.
- Protein refinement and cross-validation: the macromolecular counterparts.
Critical Analysis
Strengths
- Worked, reproducible examples. The book is built around refinements in SHELXL and describes each problem in detail, and the accompanying CD-ROM contains all the files needed to reproduce them.
- Coverage of hard cases. Alexander J. Blake of the University of Nottingham, quoted on the back cover, called the depth of treatment of twinning and disorder very valuable and not currently available elsewhere; David J. Watkin of the University of Oxford called it a high-quality text.
- Specialist authors for specialist chapters. Twinning, validation and protein refinement are handled by Herbst-Irmer, Spek, Schneider and Sawaya.
- Attention to what can go wrong. Separate chapters on artefacts and on validation deal with the reliability of a finished structure, in addition to how to refine it.
Limitations
- Tied to one program. The subtitle and the examples are about SHELXL as it was in 2006, so command details should be checked against the program's current documentation.
- Demanding material. The book addresses advanced aspects of practical refinement and is not an introduction to crystallography.
- Narrow scope. Its subject is refinement and validation; only one chapter, plus a validation chapter, concerns macromolecules.
Where It Fits in the Course
In the materials and polymer chemistry course, this is the practical crystallography title. Anthony West's Solid State Chemistry and its Applications develops bonding and crystal structures of inorganic solids and then defects and characterization; Allcock's Introduction to Materials Chemistry approaches materials from the chemist's viewpoint; and Carraher's Introduction to Polymer Chemistry and Young and Lovell's Introduction to Polymers cover polymer synthesis, structure and properties. As described, none of these is about the day-to-day work of refining a single-crystal structure.
Müller et al. is therefore a companion for readers who have learned about crystal structures from West and now need to produce or critically evaluate one from diffraction data, rather than a substitute for any of the other books.
How to Use This Book
The book suits graduate students, postdoctoral researchers and facility staff who refine small-molecule crystal structures, and advanced readers who want to evaluate published structures critically.
A practical plan:
- Start: Chapters 1 and 2 to learn the program and the logic of refinement.
- Everyday work: Chapters 3 and 4 on hydrogen atoms and atom types, then Chapter 9 on validation.
- As problems arise: Chapters 5 to 8 on disorder, pseudo-symmetry, twinning and artefacts.
- Optional: Chapters 10 and 11 for macromolecular crystallography.
Work along with the CD-ROM files in SHELXL, reproducing each refinement before attempting your own data, and check the reasoning in the later chapters against current SHELXL documentation.