It appears that when loading model/map from command line (via --pdb and --auto options) coot ignores the parameters defined in $HOME/.coot . Mine has the (set-map-sampling-rate 2.5) setting for smoother maps, but when I use the command line to load pdb/mtz files, the maps look more like sampling rate 1.5 .
Workaround is to open coot from command line, then close it, and then reopen it and accept the dialog that loads from last coot state file. Maps are smooth again. Of course, one can also load a script at the start that fixes the sampling rate. I am just saying that the expected behavior would be to import $HOME/.coot even if there are parameters in the command line. Or is it a feature? -- Coot verendus est
