SHELX

SHELX performs structure solution and refinement for small-molecule crystallography and experimental phasing of macromolecules using direct methods, density modification, and autotracing.

Key Features:

• Structure solution (SHELXS, SHELXD): SHELXS and SHELXD implement direct methods and iterative dual-space algorithms to locate atomic positions and anomalous scatterers.
• Refinement (SHELXL): SHELXL performs small-molecule refinement and supports refinement against neutron diffraction data, treatment of hydrogen atoms, determination of absolute structure, input of partial structure factors, and handling of twinned and disordered structures.
• Macromolecular phasing (SHELXC/D/E): SHELXC, SHELXD, and SHELXE provide experimental phasing workflows for SAD, MAD, SIR, SIRAS, and RIP and integrate into automated structure-solution pipelines.
• Iterative density modification and autotracing (SHELXE): SHELXE applies iterative density modification with autotracing to identify alpha-helices and common tripeptides and to assess solution status.
• CIF integration: SHELXL workflows are integrated with the CIF format so a single CIF can contain reflection data and SHELXL instructions as a complete structure archive.
• High-throughput phasing: The suite implements iterative dual-space direct methods that combine phase refinement in reciprocal space with peak picking in real space to rapidly locate anomalous scatterers for high-throughput pipelines.
• Patterson-based seeding and resolution truncation: SHELXD supports Patterson-based seeding to enhance anomalous scatterer location, with performance often improved by truncating data at ~3.0-3.5 Å.
• Performance and parallelism: Implementations emphasize speed and robustness suitable for integration into automated and high-throughput phasing workflows.

Scientific Applications:

• Small-molecule crystallography: Structure solution and refinement including neutron-data refinement, hydrogen-atom treatment, absolute-structure determination, and handling of twinned or disordered crystals.
• Macromolecular experimental phasing: Initial phasing of proteins and complexes using SAD, MAD, SIR, SIRAS, and RIP approaches and locating anomalous scatterers.
• Automated structure-solution pipelines: Integration of SHELXC/D/E and SHELXE autotracing into automated workflows for rapid structure determination.
• Data archiving and validation: Use of CIF files to archive reflection data together with SHELXL instructions for validation and deposition.

Methodology:

Computational methods explicitly include direct methods (SHELXS/SHELXD), experimental phasing protocols (SAD, MAD, SIR, SIRAS, RIP), iterative dual-space direct methods combining phase refinement in reciprocal space with peak picking in real space, Patterson-based seeding with optional data truncation (~3.0-3.5 Å), iterative density modification and autotracing (SHELXE), and the use of CIF files containing reflection data and SHELXL instructions.