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 [cid:922B93FD-C686-4CED-8281-EFF2FAFC08D2]
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://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> 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
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<https://aka.ms/o0ukef> ________________________________ 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 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/command...> 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
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/command...
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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/command...
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you Tom and Elaine. Opening on a recent version of Mac solved the problem Thank you Shubhangi On Aug 5, 2024, at 12:48 PM, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: ⓘ Informational: Infrequent Sender Weill Cornell Medicine does not regularly receive email from this sender. Be careful when clicking links or opening attachments. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/Aer6R9v1Nk4!Ng0QdH78t1CiVvLb...> Report Suspicious 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<mailto: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<mailto: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<mailto:meng@cgl.ucsf.edu>> Sent: Sunday, August 4, 2024 11:54:41 AM To: Shubhangi Agarwal <sha4008@med.cornell.edu<mailto:sha4008@med.cornell.edu>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto: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/command...
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...>
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<mailto: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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
participants (3)
-
Elaine Meng -
Shubhangi Agarwal -
Tom Goddard