Data Analysis & Structure Determination

CCP4

• As described on its website, "The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography."
• The CCP4 graphical user interface is started by typing ccp4i.

Solve/Resolve

• Solve/Resolve provides automated structure solution for MAD and MIR input files. Sample scripts are available here.
• Just about anything that Solve/Resolve scripts can do, PHENIX can do (better)!

PHENIX

• As described on its website, "PHENIX is a new software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. The PHENIX system also includes SOLVE/RESOLVE, Phaser, Textal, the CCI Applications (phenix.xtriage, phenix.refine, elbow and many more), components from Molprobity, and the Computational Crystallography Toolbox in a Python framework." The PHENIX platform allows one to perform different phases of structure solution and can be used either from the command line or through its graphical user interface.
• From the Running PHENIX section of the PHENIX documentation: "Current tasks and strategies available include:
  • Density modification: carries out a single run of RESOLVE
  • Substructure solution: runs phenix.hyss
  • Molecular replacement: computes rotation and translation functions with PHASER
  • Model building: using TEXTAL or RESOLVE
  • Ligand identification: Using RESOLVE"
• The PHENIX graphical user interface is started by typing phenix
• View the online PHENIX documentation here.

SHELX

• As descsribed on its website, "SHELX is a set of programs for crystal structure determination from single-crystal diffraction data.
• A tutorial is available here. The suite consists of the following programs:
  • SHELXS: Structure solution by Patterson and direct methods
  • SHELXC: Preparations of files for macromolecular phasing with SHELXD and SHELXE
  • SHELXD: Structure solution for difficult problems (and location of heavy atom sites)
  • SHELXE: Phases from SHELXD heavy atom sites (and density modification)
  • SHELXL: Structure refinement (use SHELXH for large structures)
  • CIFTAB: Tables for publication via (small molecule) CIF format
  • SHELXA: Post-absorption corrections (for emergency use only)
  • SHELXPRO: Protein interface to SHELX
  • SHELXWAT: Automatic water divining for macromolecules
• "The new program SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) that are used for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods."
• SHELXC reads HKL2000 .sca files. To transfer data from CCP4 it is advisable to generate .sca files using CCP4i.
• Examples of input files for MAD, SAD, SIR or SIRAS structure solution can be found on any of the beamline computing stations in /cmcf_apps/shelx/input-files or the CCP4 wiki.
• View the SHELX online manual here.

CNS

• As described on its website, "Crystallography & NMR System (CNS) ... has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights [for X-ray crystallography] include heavy atom searching, experimental phasing (including MAD and MIR), density modification, and crystallographic refinement with maximum likelihood targets."
• View the online manual and sample input files here or on any of the beamline workstations in /opt/cmcf_apps/cns_solve_1.2/inputs.

XPREP

• XPREP is available by typing xprep.
• A tutorial is available here.