Hi Dima,
Thanks, that [almost] did it. setpaths.bat now runs without an error but evidently still does not set any paths. (At least none new is shown when I use SET command to display them).
If you just run path do you see "cci_apps" in the output? setpaths.bat is supposed to add one entry to the beginning of PATH (that's all it does). You need to repeat this in each new cmd.exe (unless you are an expert and you somehow setup cmd.exe to execute cci_apps setpaths.bat automatically).
If, however, I provide path to phenix.refine.exe explicitly, it seems to run fine.
That's a good sign.
If, say, I only use phenix.refine.exe, do I need to manually set any other paths besides this executable?
No, each of the commands in the "bin" directory updates all required environment variables before launching the actual command doing the work. Ralf