Hi Dave, Those files stretch the definitions of "PDB" format -- the residue names are 5 characters, the atom names are in the wrong columns, and all the atoms in one file are named "H" and all the atoms in the other file are named "O"! However, I realize many programs write nonstandard "PDB" formats to show various things and it is useful to view them. The initial default display can be adjusted in the Preferences (Favorites... Preferences), category "New Molecules." Change "smart initial display" to "false" and click Save if you want that to apply to later uses of Chimera. Alternatively (instead of changing New Molecule preferences) you could create an alias to show nucleic acids as all atoms, for example with the command: alias ^plain nuc side atom; ~ribbon nucleic acid and in recent Chimera (v 1.5, so daily builds) that would be saved in your preferences file. You could execute that alias with the command "plain", for example: open 1bna plain or by choosing it from the top-level Aliases menu. That menu appears when "^" (start-of-line) aliases are defined in recent Chimera 1.5 builds. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 10, 2009, at 7:03 AM, David Chenoweth wrote:

Problem solved! Sorry, but it seems all I needed to do was show the atoms and bonds. Chimera is reading the file it just doesn't show anything until you tell it to show atoms and bonds. Another surprise with the new Chimera version is that it automatically displays my nucleic acid files with slab bases, filled sugars, and a backbone ribbon. Is there anyway to shut this off so I don't have to go in and manually do it each time I open a nucleic acid structure?

Thanks, Dave