[Chimera-users] demo made under Linux has bland atoms in Windows

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 17 10:35:14 PST 2007

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 C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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