Coot can read shelx .res files and write .ins files, and thus one can refine using SHELXL in a convenient manner using the function
(shelxl-refine imol . hkl-file-name)
(the hkl-file-name is an optional argument)
e.g.
(shelxl-refine 0)
or
(shelxl-refine 0 "insulin.hkl")
In the former case, coot will presume that there is a SHELX hkl file corresponding to the res file that you read in; if there is not coot will print a warning and not try to run shelxl. In the latter case, you can specify the location of the hkl file.
After shelxl has finished, coot will automatically read in the resulting res coordinates, the fcf file, convert the data to mmCIF format and read that, which generates a \sigma_A map and a difference map.
Coot creates a time stamped ins file and a time-stamped sym-link to
the hkl file in the coot-shelxl directory.
Please note that the output ins file will not be particularly useful (and thus shelxl will fail) if the input file was not in SHELX ins format.
There is a GUI for this operation under the “Extensions” menu item.