Hi Sam

What you describe is very uncommon. 
Please, describe the procedure you have used to load the files.

example:
load files "=4KKS" "=1PD6"

Hey!  I see now!
The particular 1PD6.pdb is a structure resolved by NMR as so it contains 28 
different structures (conformations)  -- taht's the reason for what you are 
seeing

You probably want to load just one model, see
http://chemapps.stolaf.edu/jmol/docs/#loadmodels



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