Sometimes, for both refinement or DLS (Distance Least Squares), when a structure has much pseudo symmetry, it can be beneficial to randomly perturb the starting positions of the atoms - especially with hand built "idealised" structure models
(Note: Shelx files can be generated from within Crystals using, from the menu, Results, Platon and if you make a mistake, you can use the Multiple UNDO within Crystals to restore from one of the previous structure models.).
The perturbation is in fractions of a unit cell (not in Angstrom), so you just calculate the average perturbation you require based on each differing cell axis.
In this example, an 0.1 Angstrom average perturbation is desired.
Load in the structure and relevant files into crystals (Crystals can import Shelx files). The red arrow points to the crystals "command line" input option which we will be using. (or the following could be made into a script file)
This is performed using an \EDIT, Perturb option within crystals. This is described in Chapter 6 of the Crystals Manual: "Atomic And Structural Parameters"
Calculate the required perturbation values (in fractional values) for the required perturbation parameter of 0.1 Angstrom. In the crystals command line, enter the following commands for x, and y-z (where these two cell axes are approximately the same):
\edit perturb 0.003 x perturb 0.006 y z end
Crystals will generate a new structure based on the above commands, plus output the "Requested Perturbation" vs the "Rms perturbation". (if you make a mistake, you can use the Multiple UNDO within Crystals to restore from one of the previous structure models).
If you want to create a Shelx file of this new structure, from the menu, use Results, Platon to generate the Shelx file.