This is a graphics driver problem related to OpenGL “instancing”, the graphics technique that renders atoms and bonds as lots of copies of spheres and cylinders.  Turning off DrawElementsInstanced will fall back to an older slower technique.

Could you use Help / Report a Bug… and say stick atoms and bonds appear black in the description?  This will give us info about your graphics, I see it in your pasted Debug OpenGL image but it would be good to document in a bug report so we no the fix if others report it.

Tom

On Oct 5, 2017, at 11:09 AM, VAZQUEZ SENTIS MARCO EUGENIO <eugenio.vazquez@usc.es> wrote:

Dear Eric, 

Thank you very much for your email. I’ve been playing around with the "Debug OpenGL on startup" option, and I finally found a way for the program to behave normally. 

So, the good settings are: 

 <PastedGraphic-4.png>

And originally I had DrawElementsInstanced checked, which made the bonds look funny. 

Thanks a lot anyway, and thank you for the great Chimera software. I’ve tried most of them, and Chimera is the one that makes the nicest images (ribbons comes close, but it’s nowhere near in ease of use). 

All the best from Spain!

e

On Oct5 2017, at 19:58, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Eugenio,

No, no one else has reported this.  We just upgraded one of the machines in our lab to High Sierra and don’t see this behavior on it.  It kind of looks like you have silhouette edges too thick.  Try going to the Effects panel of Side View (Tools->Viewing Controls->Effects) and turn off silhouette edges and see what happens.  If that helps, then maybe you could turn it back on but put a smaller value in the the “width” entry for silhouette edges.

—Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Sep 30, 2017, at 9:20 AM, VAZQUEZ SENTIS MARCO EUGENIO <eugenio.vazquez@usc.es> wrote:

Hey there, 

Thanks for the information. However, the representation of atoms is still wrong in with High Sierra. I’m attaching an image of what I see. Have you received reports like this?. Is there any fix for that?

thanks!!

<atomsallweird.jpg>

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