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SHELXL: Difference between revisions
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== Refinement of proteins == | == 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" | * 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 | * run shelxpro to obtain .ins file from .pdb file; a ligand may require the "J" option | ||
* use CGLS refinement until convergence | * 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: | * 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 | ** 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 ) | ** 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") | ** 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") | |||