Hi, maybe it's fixed in pre-release, but in our version of coot (v0.5.2):
When you load a monomer (e.g. NAP), and coot finds that
"monomer-NAP.pdb" already exists in the working directory, it will
simply load that file, rather than generating a new one.
This is a profoundly evil bug: to me, "load monomer" does not mean
"load the next convenient file in the working directory", it means "load
the monomer from the dictionary".
(Just wasted a day or so trying to find out why my NAP won't real-space