Hi John, The "New Molecules" category of Preferences controls how molecules initially appear. Choose "Favorites... Preferences" from the menu, change to category: New Molecules, adjust the settings as desired, and click Save. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules> Sounds like you want to make sure that "use new color for each model" is set to true. If by "backbone" you meant ribbon, "smart initial display" will give you protein ribbons plus atomic detail in ligand/ion binding sites. If you don't want ribbon, you would turn off smart initial display and use some of the other settings. Getting a new version of Chimera should not change your preferences -- maybe something else happened to change your preferences file or its location. Best, 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 Nov 10, 2010, at 5:55 AM, Beale, John wrote:

I have a series of pdb files that I am loading into Chimera. How can I get each file to load as a backbone structure with a different color for each? I used to be able to do this, but when I loaded a newer version of Chimera it no longer works.

I am sure that this must be a preferences issue, but I can’t figure it out. Thanks! John