Hi Pshemak 

> What is the role of the fetched files? 
> Where are the fetching instructions coming from?

I believe that should happen only when you have set "true" this 
parameter

set pdbAddHydrogens true

(please check 
http://chemapps.stolaf.edu/jmol/docs/#set_pdbaddhydrogens )

The idea is that extra information (double bonds, H atoms) is added 
for the ligands in your pdb file


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