SHELXL: Difference between revisions

There are many ways of modeling disorder using SHELXL, but for macromolecules the most convenient is to retain the same atom and residue names for the two or more components and assign a different "part number" (analogous to the PDB alternative site flag) to each component. With this technique, no change is required to the input restraints, etc. Atoms in the same component will normally have a common occupancy that is assigned to a free variable (fv). The starting values for the free variables are given, in order, on the FVAR instruction; note that there is no free variable number 1 (adding 10 fixes a parameter); the first FVAR parameter is the overall scale factor. Residues Glu_12 and Cys_38 have disordered side-chains in the example; their occupancies are tied to fv(2) (for the atoms in component [PART] 1) and to 1-fv(2) for the atoms in component 2 for Glu_12, and similarly fv(4) and 1-fv(4) for Cys_38. This ensures that the sum of occupancies for both components is held at unity. ’21.0’ is interpreted as 1.0 times fv(2), and –21.0 as 1.0 times [1-fv(2)]. This notation is not very intuitive, but it is concise and very flexible. A common example is the use of a single free variable to describe the occupancies of all the atoms in both components of a disordered sidechain, e.g.<br>

 

OG  4  ...  ...  ... -31 ...<br>

 

For a disordered serine. The starting value of the occupancy p is given as the third FVAR parameter, the two components will be assigned occupancies p and 1-p. Note  that it is desirable to split CB even if no splitting can be seen in the maps so that when hydrogens are added later with e.g. <br>

 

 

(before the first atom) the correct disordered hydrogens will be generated fully automatically. If there are three or more disorder components, then each of the common occupancies must be assigned to a separate free variable (e.g. as 51, 61 and 71), and their sum can be restrained to unity by the use of a SUMP restraint, e.g.:<br>