Dear Warren and Tsjerk,
 
Thank you for responding so quickly to my question.
 
I’m not sure what the “underlying OpenGL graphics” are on my computer.  However,  I have changed nothing on my computer.  I can open and look at both versions of the pdb file in PyMOL, look at them side-by-side, and they respond very differently.  The problem is reproducible.  I don’t how to write scripts yet, but I can give you a list of what I do.
 
I have attached the two files: Old1FOD.pdb ( the file that is easy to use) and 1FOD.pdb (the most recent version of the file from RCSB that is difficult to use).  
 
1) I double click on the pdb file and it opens automatically in PyMOL
2) In the Menu: Display: Sequence: Sequence Mode: Residues
3) Highlight residue #1
4) (sele) choose show sticks
5) (sele) choose Action: Find: Polar Contacts: To any atoms
6) (sele) choose Action: Orient or Zoom
          If I use the older version of the pdb file, the residue is zoomed in and I can easily turn the whole molecule around 360 degrees.
          If I use the newer version of the pdb file, the residue is zoomed out I cannot zoom in unless I use the left mouse button, and I cannot turn the molecule around 360 degrees.
 
Thank you for your assistance,
Nicole Lewis-Rogers


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