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SHELXL: Difference between revisions
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== Refinement of macromolecules with SHELXL == | == Refinement of macromolecules with SHELXL == | ||
SHELXL is a very general crystal structure refinement program that is equally suitable for the refinement of minerals, organometallic structures, oligonucleotides, or proteins (or any mixture thereof) against X-ray or neutron single (or twinned!) crystal data. The price of this generality is that it is somewhat slower than programs specifically written only for protein structure refinement, on the other hand a multiple-CPU version (adapted by Kay Diederichs) compensates for this. Any protein- (or DNA-) specific information must be input to SHELXL by the user in the form of refinement restraints, etc | SHELXL is a very general crystal structure refinement program that is equally suitable for the refinement of minerals, organometallic structures, oligonucleotides, or proteins (or any mixture thereof) against X-ray or neutron single (or twinned!) crystal data. The price of this generality is that it is somewhat slower than programs specifically written only for protein structure refinement, on the other hand a multiple-CPU version (adapted by Kay Diederichs) compensates for this. Any protein- (or DNA-) specific information must be input to SHELXL by the user in the form of refinement restraints, etc. <br> | ||
Despite this generality, it must be emphasized that SHELXL is not suitable for refinements at resolutions lower than about 2.0 Å because, unlike [[Refmac]] and [[phenux.refne]], it does not provide (side-chain) torsion angle restraints, and that a least-squares refinement program such as SHELXL will suffer more from model bias than a program based on maximum likelihood. Also the Babinet bulk solvent model used in SHELXL is in need of improvement. Almost always the initial refinement will have been performed with another program and SHELXL will be used for the final refinement, perhaps involving extension to very high resolution, modeling of disorder, anisotropic refinement and the least-squares estimation of parameter errors. Thus the starting point for a SHELXL refinement will usually be a PDB format file from the previous refinement. Even when SHELXL has to be used for the refinement of a non-merohedrally twinned structure at lower resolution, the starting model is likely to be in the form of a PDB file from a molecular replacement solution.<br> | Despite this generality, it must be emphasized that SHELXL is not suitable for refinements at resolutions lower than about 2.0 Å because, unlike [[Refmac]] and [[phenux.refne]], it does not provide (side-chain) torsion angle restraints, and that a least-squares refinement program such as SHELXL will suffer more from model bias than a program based on maximum likelihood. Also the Babinet bulk solvent model used in SHELXL is in need of improvement. Almost always the initial refinement will have been performed with another program and SHELXL will be used for the final refinement, perhaps involving extension to very high resolution, modeling of disorder, anisotropic refinement and the least-squares estimation of parameter errors. Thus the starting point for a SHELXL refinement will usually be a PDB format file from the previous refinement. Even when SHELXL has to be used for the refinement of a non-merohedrally twinned structure at lower resolution, the starting model is likely to be in the form of a PDB file from a molecular replacement solution.<br> | ||