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SHELXL: Difference between revisions
chiral volumes
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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. <br> | 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 [[PHENIX|phenix.refine]], 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 | 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 [[PHENIX|phenix.refine]], 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 maximumlikelihood. 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> | ||
== Input files for SHELXL == | == Input files for SHELXL == | ||
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The PRODRG server: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ is recommended for generating restraints in SHELX format for ligands etc; the "J" option in SHELXPRO can also be useful for this if a model is already available. File of DNA and RNA restraints are available from the SHELX download site.<br> | The PRODRG server: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ is recommended for generating restraints in SHELX format for ligands etc; the "J" option in SHELXPRO can also be useful for this if a model is already available. File of DNA and RNA restraints are available from the SHELX download site.<br> | ||
== Chiral volumes == | |||
SHELXL defines a chiral volume as the volume of the 'unit-cell' that can be constructed using the three interatomic | |||
vectors from the atom in question; this can be calculated as a determinant using orthognal cartesian coordinates.SHELXL | |||
restricts chiral volumes to cases where an atom makes exactlythree bonds to other non-hydrogen atoms; hydrogen atoms are | |||
ignored. The sign is determined by evaluating the determinantwith the rows representing the three vectors in the order of | |||
their ASCII codes, and so is independent of the order of theatoms in the input file. This means that the alpha carbon in | |||
the 19 standard chiral L-amino-acids will always have a chiralvolume of about +2.5 (using the Cahn-Ingold-Prelog R and S conventional would have required L-Cys to have the opposite sign).CB of Ile has a (SHELX) chiral volume of 2.495 but CB | |||
of Thr is -2.628. However the CHIV instruction in SHELXL also has other uses, e.g. | |||
CHIV_VAL C | |||
CHIV_VAL 2.516 CA | |||
CHIV_VAL -2.622 CB | |||
This restrains the chiral volume of the carbonyl carbon to be zero (the default) with a default esd (0.1 A^3), i.e.restrains | |||
it to be planar. CB is not chiral for valine, but the above restraint makes sure that CG1 and CG2 are named conventionally | |||
(the RSCB now use this idea to check the naming of H-atoms in CH2 groups, which is one of the reasons why I always remove the hydrogens before depositing the structure (they are always recalculated anyway before use, e.g. by MolProbity). And | |||
if you wanted all the alpha-carbons for the alanines to havethe same chiral volume but would like to refine its value, a | |||
SHELX 'free-variable' can be used (here #3): | |||
CHIV_ALA 31 CA | |||
(i.e. 1*fv(3)); if there is a D-Ala in the structure as well: | |||
CHIV_DAL 29 CA | |||
(i.e. -1*fv(3)). | |||