hide silhouettes for pseudobonds and mesh
Hi all, Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument. One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist. Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Daniel, Sorry, no ... silhouettes are a global setting, either all off or all on. Sometimes you can fiddle with the depthJump parameter, e.g. if you are getting too many contours on a surface, but I don't think that addresses the problem with mesh: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> See these previous posts on this topic, including some tips on possible alternatives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 Apr 11, 2024, at 12:12 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument.
One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist.
Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids.
Regards, Daniel
Hi Daniel, You can effectively get rid of cartoon tethers by scaling them to zero, e.g.: cartoon tether scale 0 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> As a side note, they are not pseudobonds: if they were pseudobonds you could use a hide command to undisplay them, e.g. hide targ p ...or use disclosure triangles in the Model Panel to see the pseudobond model listing and use the show/hide checkbox there. I hope this helps, Elaine
On Apr 11, 2024, at 8:13 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Sorry, no ... silhouettes are a global setting, either all off or all on. Sometimes you can fiddle with the depthJump parameter, e.g. if you are getting too many contours on a surface, but I don't think that addresses the problem with mesh: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>
See these previous posts on this topic, including some tips on possible alternatives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
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 Apr 11, 2024, at 12:12 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument.
One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist.
Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids.
Regards, Daniel
Hi Elaine, Thank you so much for the suggestion of setting the cartoon tether scale to zero. That is a better option than opacity zero since it also hides the silhouettes. I had worked out a workaround by copying the molecule using the combine command and then showing the cartoon for that and the atoms for the original model, but this is much more convenient. Regards, Daniel On 2024-04-11, 18:37, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Daniel, You can effectively get rid of cartoon tethers by scaling them to zero, e.g.: cartoon tether scale 0 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether>> As a side note, they are not pseudobonds: if they were pseudobonds you could use a hide command to undisplay them, e.g. hide targ p ...or use disclosure triangles in the Model Panel to see the pseudobond model listing and use the show/hide checkbox there. I hope this helps, Elaine
On Apr 11, 2024, at 8:13 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Daniel, Sorry, no ... silhouettes are a global setting, either all off or all on. Sometimes you can fiddle with the depthJump parameter, e.g. if you are getting too many contours on a surface, but I don't think that addresses the problem with mesh: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>>
See these previous posts on this topic, including some tips on possible alternatives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>/message/NFNED62LWN6M3QVABBRTVSS5C2QTFN2V/> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>/message/N4B7ZBCXLF55UWQ7NVGGKOEKGHOEQG5C/> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>/message/SJ6AJTNOBJR2U2GRNLG7J5TNPWPAPJPW/>
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 Apr 11, 2024, at 12:12 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi all,
Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument.
One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist.
Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>/message/U4IHTWL7O7RDWVGX4RXGJHKUY7LQFMKY/ I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids.
Regards, Daniel
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participants (2)
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Daniel Larsson -
Elaine Meng