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SHELXL: Difference between revisions
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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 | 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 exactlythree bonds to other non-hydrogen atoms; hydrogen atoms are | ||
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. | ||
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 C | ||
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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 | 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 SHELXL 'free-variable' can be used (here #3): | ||
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 | |||
CHIV_ALA 31 CA | CHIV_ALA 31 CA | ||
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(i.e. -1*fv(3)). | (i.e. -1*fv(3)). | ||
== Least-squares refinement algebra == | == Least-squares refinement algebra == | ||