Thank you Conrad and Jaime for you answers.

The debug options indeed fixed the problem. Instead of disabling DrawElementsInstanced, disabling Shading also seems to work.

Jethro

2014-10-08 23:04 GMT+02:00 Jaime Stark <jlstark@wisc.edu>:

I was seeing this problem too in Yosemite. It’s easily fixed by turning on the “Debug OpenGL on startup” as Conrad suggests. When you next start Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. That will fix the dim coloring for small molecules on Yosemite for now.

Jaime

===================================
Jaime L. Stark, Ph.D.
Postdoctoral Research Associate at NMRFAM

University of Wisconsin - Madison
Department of Biochemistry

DeLuca Biochemical Laboratories
Room B160H

433 Babcock Drive
Madison, WI  53706
Email: jlstark@wisc.edu
Phone: (608) 262-0459
Website: http://www.nmrfam.wisc.edu
===================================

On Oct 8, 2014, at 3:48 PM, Conrad Huang <conrad@cgl.ucsf.edu> wrote:

Unfortunately, we have not tested Chimera on Yosemite yet.  It is highly likely that there is some OpenGL issue given the images that you are seeing.  We will try to get to this soon, but we're pretty tight on programmer resources.

If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup".  The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html).  If you discover anything, please let us know.

Conrad

On 10/8/2014 2:31 AM, Jethro Hemmann wrote:

Hi,

I'm currently using Chimera on my Macbook running the public beta of
Yosemite.

The colors of the molecules appear very dim and they are hard to
recognize, as can be seen in the attached screenshot. In this example,
the lipid chains are colored orange, while the water molecules should by
cyan.
The colors in the menu Actions --> Color seem to appear with their
correct brightness, although.

I also tried the daily build of the alpha version of Chimera, but the
problem persists.

Is this problem related to Yosemite? Or do I have to adjust some settings?

Thanks a lot,

Jethro


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