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SHELXL: Difference between revisions
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→Chiral volumes
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SHELXL defines a chiral volume as the volume of the 'unit-cell' that can be constructed using the three interatomic | 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 orthogonal cartesian coordinates. SHELXL restricts chiral volumes to cases where an atom makes | vectors from the atom in question; this can be calculated as a determinant using orthogonal cartesian coordinates. SHELXL restricts chiral volumes to cases where an atom makes exactly three bonds to other non-hydrogen atoms; hydrogen atoms are | ||
ignored. The sign is determined by evaluating the | ignored. The sign is determined by evaluating the determinant with the rows representing the three vectors in the order of their ASCII codes, and so is independent of the order of the atoms 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 convention would have required L-Cys to have the opposite sign). CB of Ile has a 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 C''' | ||
CHIV_VAL 2.516 CA | '''CHIV_VAL 2.516 CA''' | ||
CHIV_VAL -2.622 CB | '''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 | 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 the hydrogens should be removed 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 have the same chiral volume but would like to refine its value, a SHELXL 'free-variable' can be used (here #3): | ||
CHIV_ALA 31 CA | '''CHIV_ALA 31 CA''' | ||
(i.e. 1*fv(3)); if there is a D-Ala in the structure as well: | (i.e. 1*fv(3)); if there is a D-Ala in the structure as well: | ||
CHIV_DAL 29 CA | '''CHIV_DAL 29 CA''' | ||
(i.e. -1*fv(3)). | (i.e. -1*fv(3)). | ||