On Feb 16, 2007, at 7:55 PM, Kenward Vaughan wrote:

For me, the byatom coloration is there to begin with under Linux. The ach shows up colored properly, as does the acetylcholinesterase.

Aha!! Problem solved!! I am 99.99% sure the difference is your preferences file. The demo itself does not say to color by element when the structure is opened. However, there is a New Molecules section of the Preferences in which you can say structures should be colored that way when they are opened. Most likely you have this set on your home Linux machine, but not in the Chimera preferences used on the Windows machines. Months ago we discussed the need for some way to indicate that preferences should be bypassed at startup and/or when opening structures. This option would be appropriate for use with demos or scripts to be shared among multiple users each having some arbitrary set of preferences settings. However, this option hasn't been added (nor are we sure how best to implement it)... thanks for the additional motivation to revisit that issue! The demos included with Chimera were made in a directory with a default preferences file. It is likely, however, that some users with nondefault New Molecules preferences have played them back and gotten a result different than intended.

I've noticed rotation is slow under Windows, but v. nice with Linux (about 7 seconds total).

It depends on the graphics capabilities of the system. It is slow on our home desktop computer (>5 years old - you can almost hear gears grinding) but fast on my laptop (1-2 years old). Happy demoing and please do contact us with any problems or suggestions, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html