I downloaded a similar file from 
ftp://ftp.pdbj.org/pub/pdb/data/structures/all/pdb/pdb163l.ent.gz
...
and with the current version of file-roller and jmol, I could not reproduce 
this bug.
So I consider it as non-reproducible, and will close it.

** Changed in: file-roller (Ubuntu)
       Status: New => Fix Released

** Changed in: jmol (Ubuntu)
       Status: New => Fix Released

** Changed in: rasmol (Ubuntu)
       Status: New => Fix Released

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https://bugs.launchpad.net/bugs/1159492

Title:
  science PDB file is not processed correctly after extraction

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