SHELXL

Refinement of proteins (to get e.g. standard uncertainties on distances)

• go to http://shelx.uni-ac.gwdg.de/SHELX and read "SHELX-97 Manual as PDF", "Mini-protein refinement tutorial" as well as "P1-Lysozyme refinement tutorial", "Thomas Schneider's FAQs" and "FAQs: Macromolecules"
• run shelxpro to obtain .ins file from .pdb file; a ligand may require the "J" option
• use "CGLS x y" refinement until convergence; the final run should be "CGLS x" only.
• a final job to get standard uncertainties (s.u., formerly e.s.d.) on all geometric parameters (see Q21 in "FAQs: Macromolecules"):
  • change CGLS x y to REM CGLS x y
  • insert lines L.S. 1, DAMP 0 0 and BLOC 1 (or e.g. BLOC N_1 > LAST )
  • delete all restraints: lines begining with SIMU, DELU, ISOR, BUMP, DFIX, DANG, CHIV, FLAT (from "Mini-protein refinement tutorial")
  • BOND, RTAB, HTAB and MPLA instructions may be needed to define the dependent parameters for which esds are required (from "FAQs: Macromolecules")