SHELXL: Difference between revisions

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* 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"
* 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
* run shelxpro to obtain .ins file from .pdb file; a ligand etc. may require the "J" option or http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ to get restraints in SHELX format
* use "CGLS x y" refinement until convergence; the last run should be "CGLS x" only.
* use "CGLS x y" refinement until convergence; the last 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"):
* 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 )
** remove all restraints: lines begining with SIMU, DELU, ISOR, BUMP, DFIX, DANG, CHIV, FLAT (from "Mini-protein refinement tutorial"). <br>(Editor's) Note a): NCSY then should also be removed, right? b) all of this is only useful for high-resolution work (let's say 1.4 A). At low to medium resolution, my typical question would rather be: what are the s.u. on the ''unrestrained'' distances between atoms x and y, given that these atoms are covalently bound to other atoms with restraints? In other words, I would keep all geometric restraints and ask "how much is the s.u. on this unrestrained distance based on crystallographic data (reflections to some resolution) for this model (with its R-factor, B-factors and restraints)?".
** remove all restraints: lines begining with SIMU, DELU, ISOR, BUMP, DFIX, DANG, CHIV, FLAT and NCSY (from "Mini-protein refinement tutorial"). This is only useful for high-resolution work (let's say 1.4 A). Alternatively, one can determine standard uncertainties in the Bayesian sense that take all available knowledge into account by retaining all the restraints. This may be done at more modest resolution (say 2.5A or better). To obtain mean values and s,u.s of e.g. distances or chiral volumes that occur several times in a structure, use DFIX or CHIV with "free variables". BOND, RTAB, HTAB and MPLA instructions may be needed to define the dependent parameters for which esds are required (from "FAQs: Macromolecules"). As an example, BIND FE_5001 NE2_123 together with BOND FE_5001 NE2_123 would enter the distance between FE_5001 and NE2_123 into the connectivity table, and would print out the distance and its s.u. into the .lst file.
** BOND, RTAB, HTAB and MPLA instructions may be needed to define the dependent parameters for which esds are required (from "FAQs: Macromolecules"). As an example, BIND FE_5001 NE2_123 together with BOND FE_5001 NE2_123 would enter the distance between FE_5001 and NE2_123 into the connectivity table, and would print out the distance and its s.u. into the .lst file.

Revision as of 21:05, 13 March 2008

Refinement of proteins (e.g. to get 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 etc. may require the "J" option or http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ to get restraints in SHELX format
  • use "CGLS x y" refinement until convergence; the last 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 )
    • remove all restraints: lines begining with SIMU, DELU, ISOR, BUMP, DFIX, DANG, CHIV, FLAT and NCSY (from "Mini-protein refinement tutorial"). This is only useful for high-resolution work (let's say 1.4 A). Alternatively, one can determine standard uncertainties in the Bayesian sense that take all available knowledge into account by retaining all the restraints. This may be done at more modest resolution (say 2.5A or better). To obtain mean values and s,u.s of e.g. distances or chiral volumes that occur several times in a structure, use DFIX or CHIV with "free variables". BOND, RTAB, HTAB and MPLA instructions may be needed to define the dependent parameters for which esds are required (from "FAQs: Macromolecules"). As an example, BIND FE_5001 NE2_123 together with BOND FE_5001 NE2_123 would enter the distance between FE_5001 and NE2_123 into the connectivity table, and would print out the distance and its s.u. into the .lst file.
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