There is a ticket for this request in our database, #174. It is old, but helpful to know that more people are interested in the feature. I’ve wanted it too!

http://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/176

Best, Elaine

On Mar 4, 2020, at 8:16 AM, Elaine Meng meng@cgl.ucsf.edu wrote:

Hi Aritz, You are not doing anything wrong — currently the silhouette edges are “immune” from the depth-cuing fog, and there is no option to also fade them. It has been requested by a few users, but there is no option yet, sorry. Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Mar 4, 2020, at 6:00 AM, Aritz Roa Eguiara aritz.eguiara@cpr.ku.dk wrote:

Dear ChimeraX team,

I write you to ask about the depth cueing option. I have a structure with the silhouette true option and now I want to change the depth cueing to obtain a slice of the structure but with some of the fog coming from the background. The cartoon color disappear gradually as expected, however the black line of the silhouette is 100% or nothing, is there anything I am doing wrong or is it what I should expect? Is there anyway to obtain also that smooth disappearing of the silhouette?

Thank you for your help.

All the best, Aritz

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ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Hi Aritz,

The current ChimeraX silhouette drawing code does not know the depth of the silhouette and therefore cannot dim it with depth cueing. It is possible to improve the code so it know the depth of the silhouettes but I have not had time to work on that because of a hundred competing improvements and new features. It is a bit tricky make silhouettes have depth because it requires new low level graphics OpenGL shader code to be written. I hope to do it some day.

Tom

On Mar 4, 2020, at 8:16 AM, Elaine Meng wrote:

Hi Aritz, You are not doing anything wrong — currently the silhouette edges are “immune” from the depth-cuing fog, and there is no option to also fade them. It has been requested by a few users, but there is no option yet, sorry. Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Mar 4, 2020, at 6:00 AM, Aritz Roa Eguiara wrote:

Dear ChimeraX team,

I write you to ask about the depth cueing option. I have a structure with the silhouette true option and now I want to change the depth cueing to obtain a slice of the structure but with some of the fog coming from the background. The cartoon color disappear gradually as expected, however the black line of the silhouette is 100% or nothing, is there anything I am doing wrong or is it what I should expect? Is there anyway to obtain also that smooth disappearing of the silhouette?

Thank you for your help.

All the best, Aritz

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ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Hi Steve, For setting and reporting the current clipping plane offsets, see "clip" and "clip list" respectively.

http://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 5, 2020, at 12:06 PM, Steve Chou stevezchou@gmail.com wrote:

Hi Tom, Can we GET and SET the positions (float number) of the two vertical bars (near & far) on COMMAND LINE? Thank you for this help and others! Steve