liminfoSHELX Reference
Free reference guide: SHELX Reference
About SHELX Reference
The SHELX Reference is a detailed command reference for the SHELX suite of crystallographic programs, the most widely used software for small-molecule and macromolecular crystal structure determination and refinement. It covers general setup commands (TITL, CELL, ZERR, LATT, SYMM, SFAC, UNIT) for defining unit cell parameters, space group symmetry, and elemental composition, along with structure determination methods using SHELXS (direct methods via TREF, Patterson method via PATT) and SHELXD (dual-space iteration for larger molecules).
The refinement section details SHELXL commands for least-squares refinement including cycle control (L.S., CGLS), weighting scheme parameters (WGHT with the a,b coefficients for w = 1/[sigma^2(Fo^2) + (aP)^2 + bP]), free variable management (FVAR for scale factors and occupancy refinement), anisotropic displacement parameters (ANIS), disorder modeling with PART sections and linked FVAR occupancies, and extinction correction (EXTI).
Restraints and constraints are covered extensively: DFIX for bond distance restraints, FLAT for planarity, SADI for similar distances, SIMU for similar anisotropic displacement parameters within 1.7 angstroms, DELU for Hirshfeld rigid-bond restraints, and ISOR for near-isotropic ADP restraints. The output section covers CIF generation (ACTA), residual density analysis (PLAN Q-peaks), bond/angle listings (LIST 6), and refinement quality assessment through R1 and wR2 indicators.
Key Features
- Unit cell setup commands: CELL wavelength and parameters, ZERR molecular count and errors, LATT lattice type, SYMM symmetry operations
- Structure determination via SHELXS direct methods (TREF), Patterson method (PATT), and SHELXD dual-space approach (FIND, MIND, TRYS)
- Least-squares refinement controls: L.S./CGLS cycle count, WGHT weighting scheme with automatic a,b parameter suggestion
- Disorder modeling with PART sections, linked FVAR occupancy variables, and complementary occupancy constraints
- Bond distance restraints (DFIX), planarity (FLAT), similar distances (SADI) with sigma values and multi-bond syntax
- ADP restraints: SIMU for similar Uij within 1.7A, DELU rigid-bond (Hirshfeld test), ISOR near-isotropic constraint
- Output controls: ACTA for CIF generation, PLAN for Q-peak analysis, LIST 6 for detailed bond/angle tables
- R-factor interpretation: R1 quality thresholds (< 0.05 good, < 0.03 excellent) and wR2 relationship to R1
Frequently Asked Questions
What programs are in the SHELX suite?
The SHELX suite consists of SHELXS for structure solution by direct methods or Patterson methods, SHELXD for structure solution by dual-space methods (particularly useful for heavy-atom substructures and larger molecules), and SHELXL for structure refinement by full-matrix least-squares on F^2. The input file format (.ins) and reflection data (.hkl) are shared across the programs.
How do I set up the unit cell in a SHELX .ins file?
Use CELL followed by the radiation wavelength (0.71073 for Mo Ka, 1.54178 for Cu Ka) and the six cell parameters (a, b, c, alpha, beta, gamma in angstroms and degrees). Then specify ZERR with Z (molecules per cell) and standard deviations. Set the lattice type with LATT (1=P to 7=C; positive for centrosymmetric, negative for non-centrosymmetric) and add SYMM lines for additional symmetry generators.
What is the difference between direct methods and Patterson methods?
Direct methods (TREF in SHELXS) use statistical phase relationships to determine crystal structures and work well for small to medium-sized molecules with light atoms. Patterson methods (PATT) locate heavy atoms from the Patterson function (auto-convolution of electron density) and are preferred when the structure contains one or a few heavy atoms whose positions can bootstrap the solution.
How does disorder modeling work with PART and FVAR?
PART n assigns atoms to disorder component n. FVAR defines free variables where the first is the overall scale factor. Occupancies are linked using notation like 21.0000 (FVAR(2)*1.0) for part 1 and -21.0000 (1-FVAR(2)*1.0) for part 2, ensuring complementary occupancies that sum to 1.0. Each PART group should return to PART 0 after defining its atoms.
When should I use SIMU vs. DELU restraints?
SIMU restrains adjacent atoms (within 1.7 angstroms by default) to have similar anisotropic displacement parameters (Uij), which is physically reasonable for neighboring atoms in a rigid structure. DELU applies the Hirshfeld rigid-bond test, restraining the displacement components along each bond to be equal for both bonded atoms. DELU is stricter and more physically justified; using both together is common practice for problematic structures.
What R-factor values indicate a good crystal structure?
R1 (conventional R-factor on F) below 0.05 is considered good quality, and below 0.03 is excellent for small-molecule structures. wR2 (weighted R-factor on F^2) is typically 2-3 times R1. The goodness-of-fit (GooF) should be close to 1.0. Very high R-factors may indicate incorrect space group, unmodeled disorder, twinning, or data quality issues.
How do I generate a CIF file for journal submission?
Add the ACTA instruction to your .ins file. After refinement, SHELXL generates a .cif file containing all structural data, refinement parameters, and atomic coordinates in the standard Crystallographic Information Framework format. Run checkCIF validation through the IUCr website before submission to identify potential issues.
What is HKLF 4 vs. HKLF 3 data format?
HKLF 4 specifies that reflection data is in h, k, l, F^2, sigma(F^2) format, which is the standard for SHELXL refinement on F-squared. HKLF 3 uses h, k, l, F, sigma(F) format for refinement on F (less common now). HKLF 4 is recommended as refinement on F^2 is statistically more rigorous and handles weak reflections better.