The difference between the two files is that one of them is a single monomer whereas the other contains all 60 copies of the virion capsid biological unit.  The problems you are experiencing are related to that fact that you are loading about 320,000 atomic coordinates with the new file as opposed to 5,300 atoms in the old file. 
The "new" file you downloaded from the protein database is a complete biological unit, not the normal PDB entry.
set all_states
to see what I mean.
When you are clicking on a single residue, you are really referring to all sixty copies of that residue, hence the unexpected behavior...

From: [] On Behalf Of Nicole Lewis-Rogers
Sent: Wednesday, September 05, 2007 9:32 AM
Subject: Re: [PyMOL] Problem with using Zoom command & difficulty movingmolecules

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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