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SHELXL: Difference between revisions
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== Refinement of macromolecules with SHELXL == | == Refinement of macromolecules with SHELXL == | ||
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== Output files | == SHELXL Output files == | ||
SHELXL writes a updated parameter file with the extension .res in the same format as the input .ins file, a .pdb file with the new atom coordinates (unfortunately one has to add the space group to the CRYST1 record before Coot can read this file) and an output .fcf file containing phased reflection data in CIF format. This file can be used for depositing the reflection data with the PDB, and both the .res and the .fcf file can be read by Coot to enable the refined atoms and σ<sub>A</sub> weighted maps to be displayed directly. <br? | SHELXL writes a updated parameter file with the extension .res in the same format as the input .ins file, a .pdb file with the new atom coordinates (unfortunately one has to add the space group to the CRYST1 record before Coot can read this file) and an output .fcf file containing phased reflection data in CIF format. This file can be used for depositing the reflection data with the PDB, and both the .res and the .fcf file can be read by Coot to enable the refined atoms and σ<sub>A</sub> weighted maps to be displayed directly. <br? | ||
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<b>FLAT_* 0.3 O_- CA_- N C_- CA</b><br> | <b>FLAT_* 0.3 O_- CA_- N C_- CA</b><br> | ||
restrains N and CA of each amino-acid and O, CA and C of the preceding residue to lie in a plane with a relatively large esd (0.3) (peptide planarity). | restrains N and CA of each amino-acid and O, CA and C of the preceding residue to lie in a plane with a relatively large esd (0.3) (peptide planarity).<br> | ||
== Least-squares refinement algebra == | |||
The original SHELX refinement algorithms were modeled closely on those described by Cruickshank (1970). For macromolecular refinement, an alternative to (blocked) full-matrix refinement is provided by the conjugate-gradient solution of the least-squares normal equations as described by Hendrickson & Konnert (1980), including preconditioning of the normal matrix that enables positional and displacement parameters to be refined in the same cycle. The structure factor derivatives contribute only to the diagonal elements of the normal matrix, but all restraints contribute fully to both the diagonal and non-diagonal elements, although neither the Jacobian nor the normal matrix itself are ever generated by SHELXL. The parameter shifts are modified by comparison with those in the previous cycle to accelerate convergence whilst reducing oscillations. Thus, a larger shift is applied to a parameter when the current shift is similar to the previous shift, and a smaller shift is applied when the current and previous shifts have opposite signs.<br> | |||
SHELXL refines against F<sup>2</sup> rather than F, which enables all data to be used in the refinement with weights that include contributions from the experimental uncertainties, rather than having to reject F-values below a preset threshold; there is a choice of appropriate weighting schemes. Provided that reasonable estimates of σ(F<sup>2</sup>) are available, this enables more experimental information to be employed in the refinement; it also facilitates refinement against data from twinned crystals.<br> | |||
== Full-matrix estimates of standard uncertainties == | |||