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The black speckles when you turn on silhouettes is a bug in your graphics driver present in a specific Intel Mac laptop model
from around 2020. We have no way of fixing this and Apple will probably never fix it. Newer Mac M1//M2/M3 models do not have the problem. To save an image with silhouettes without artifacts you have to use another computer. You can save a session (.cxs file) and copy it to another computer to make an image.
Tom
> On Aug 5, 2024, at 8:24 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Well, you have to choose a compromise value for silhouettes depthJump. If you use a small value to show a specific outline then you may get many other lines you don't want.
>
> Elaine
>
>
>> On Aug 4, 2024, at 11:02 AM, Shubhangi Agarwal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> I tried using 0.1 but that doesn’t give me the outline for the region in front that I wanto highlight so I am using depth cue of 0.05
>>
>> Get Outlook for iOS
>> From: Elaine Meng <meng@cgl.ucsf.edu>
>> Sent: Sunday, August 4, 2024 11:54:41 AM
>> To: Shubhangi Agarwal <sha4008@med.cornell.edu>
>> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
>> Subject: [EXTERNAL] Re: [chimerax-users] Silhoutte
>>
>> Hi Shubhangi,
>> I don't know why your silhouettes are generating so many extra lines, but there is a parameter you can adjust, "depthJump", e.g. command:
>>
>> graphics silhouettes true depthJump 0.1
>>
>> If you just use command:
>>
>> graphics silhouettes
>>
>> ...it will say in the Log what settings you have currently. See help for this command:
>> <
>> https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html*silhouettes__;Iw!!Aer6R9v1Nk4!4q8UT5QJIy3-NJSFL1XUAQZGrSCXhwVgvpKBewr5CGj1mcKioxTPsRbfIDqnEJ1-nwYdAal-ygf-0BIG6bc-0U6r$
>>>
>>
>> However, since your display was also showing lots of little dots, maybe there is some other problem such as with your graphics driver.
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Resource for Biocomputing, Visualization, and Informatics
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>>> On Aug 3, 2024, at 6:46 AM, Shubhangi Agarwal via ChimeraX-users <
>> chimerax-users@cgl.ucsf.edu
>>> wrote:
>>>
>>> Dear developers,
>>>
>>> I am trying to outline surfacerepresentation of my protein structure with the silhouette feature but it gives me black dashes along rest of the surface which I don’t want, how can I just use the black borderline feature for my surface and protein?
>>> Figure attached below.
>>>
>>> Thank you
>>>
>>> Shubhangi
>>>
>>
>>
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