multiple isosurfaces for one map
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome.
Regards, Daniel
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Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. Regards, Daniel
Hi Elaine,
Thank you for pointing out that if one right-clicks in the histogram of the volume in the volume viewer window, one can add a level. It was also easy to add another surface by giving multiple level arguments to the volume command.
Is it possible to show one contour as surface and one as mesh?
Regards, Daniel
On 2020-11-19, at 17:17, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. 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/
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Hi Daniel,
Yes, I just tried, and saw it’s possible to display both with distinct styles and colors. In the volume viewer, the style and color options will only apply to the threshold cursor you moved or clicked last. I did not pay close attention to what the log reported when I tried, but it printed commands, so there is definitely a way to achieve the same thing with commands.
I hope this helps,
Guillaume
On 4 Dec 2020, at 15:08, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Hi Elaine,
Thank you for pointing out that if one right-clicks in the histogram of the volume in the volume viewer window, one can add a level. It was also easy to add another surface by giving multiple level arguments to the volume command.
Is it possible to show one contour as surface and one as mesh?
Regards, Daniel
On 2020-11-19, at 17:17, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. 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
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Hi Daniel, If you mean for the same dataset (multiple levels on the same histogram), in my tests the isosurfaces are all the same style... so if you change one isosurface from mesh to surface using the Volume Viewer interface, the other levels on the same dataset will also change from mesh to surface.
However, I could use the "surface style" command after looking in the Model panel to see the submodel numbers of the different isosurfaces.
For example, I had volume #2 with isosurfaces #2.1 and #2.2. In ChimeraX it did not work to specify #2.1 or #2.2 in the "volume" command because they are surface models, but I could use commands like:
surface style #2.1 solid
...however, as soon as I moved the threshold in the Volume Viewer, it reverted back to "mesh" since that was the chosen volume style.
So if you really want to be able to adjust the level and keep it different style from the other level, I believe you would need to open the dataset twice and treat it as if it were two different datasets.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2020, at 7:44 AM, Guillaume Gaullier guillaume@gaullier.org wrote:
Hi Daniel,
Yes, I just tried, and saw it’s possible to display both with distinct styles and colors. In the volume viewer, the style and color options will only apply to the threshold cursor you moved or clicked last. I did not pay close attention to what the log reported when I tried, but it printed commands, so there is definitely a way to achieve the same thing with commands.
I hope this helps,
Guillaume
On 4 Dec 2020, at 15:08, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Hi Elaine,
Thank you for pointing out that if one right-clicks in the histogram of the volume in the volume viewer window, one can add a level. It was also easy to add another surface by giving multiple level arguments to the volume command.
Is it possible to show one contour as surface and one as mesh?
Regards, Daniel
On 2020-11-19, at 17:17, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. 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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Daniel,
Elaine is right, the Volume Viewer GUI only handles all surfaces of one volume model having the same style (surface or mesh). ChimeraX can display the different surfaces in different styles using commands but not with the GUI. The reason the GUI doesn't allow it is it makes the user interface too complicated. I try to keep the user interface simple to give best serve most users. I'll make a feature request for handling mixed mesh and surface in the gui and maybe some day I'll think of a way to add it that keeps it simple.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4019
Tom
On Dec 4, 2020, at 8:30 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, If you mean for the same dataset (multiple levels on the same histogram), in my tests the isosurfaces are all the same style... so if you change one isosurface from mesh to surface using the Volume Viewer interface, the other levels on the same dataset will also change from mesh to surface.
However, I could use the "surface style" command after looking in the Model panel to see the submodel numbers of the different isosurfaces.
For example, I had volume #2 with isosurfaces #2.1 and #2.2. In ChimeraX it did not work to specify #2.1 or #2.2 in the "volume" command because they are surface models, but I could use commands like:
surface style #2.1 solid
...however, as soon as I moved the threshold in the Volume Viewer, it reverted back to "mesh" since that was the chosen volume style.
So if you really want to be able to adjust the level and keep it different style from the other level, I believe you would need to open the dataset twice and treat it as if it were two different datasets.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2020, at 7:44 AM, Guillaume Gaullier guillaume@gaullier.org wrote:
Hi Daniel,
Yes, I just tried, and saw it’s possible to display both with distinct styles and colors. In the volume viewer, the style and color options will only apply to the threshold cursor you moved or clicked last. I did not pay close attention to what the log reported when I tried, but it printed commands, so there is definitely a way to achieve the same thing with commands.
I hope this helps,
Guillaume
On 4 Dec 2020, at 15:08, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Hi Elaine,
Thank you for pointing out that if one right-clicks in the histogram of the volume in the volume viewer window, one can add a level. It was also easy to add another surface by giving multiple level arguments to the volume command.
Is it possible to show one contour as surface and one as mesh?
Regards, Daniel
On 2020-11-19, at 17:17, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. 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
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An alternative to having one level as mesh and the other as surface, without having to load the same map twice, is to display both levels as surface, with different colors, and with transparency for the lower level. I find it as easy to look at as having the lower level as mesh and the higher one as surface.
Guillaume
On 4 Dec 2020, at 20:12, Tom Goddard goddard@sonic.net wrote:
Hi Daniel,
Elaine is right, the Volume Viewer GUI only handles all surfaces of one volume model having the same style (surface or mesh). ChimeraX can display the different surfaces in different styles using commands but not with the GUI. The reason the GUI doesn't allow it is it makes the user interface too complicated. I try to keep the user interface simple to give best serve most users. I'll make a feature request for handling mixed mesh and surface in the gui and maybe some day I'll think of a way to add it that keeps it simple.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4019
Tom
On Dec 4, 2020, at 8:30 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, If you mean for the same dataset (multiple levels on the same histogram), in my tests the isosurfaces are all the same style... so if you change one isosurface from mesh to surface using the Volume Viewer interface, the other levels on the same dataset will also change from mesh to surface.
However, I could use the "surface style" command after looking in the Model panel to see the submodel numbers of the different isosurfaces.
For example, I had volume #2 with isosurfaces #2.1 and #2.2. In ChimeraX it did not work to specify #2.1 or #2.2 in the "volume" command because they are surface models, but I could use commands like:
surface style #2.1 solid
...however, as soon as I moved the threshold in the Volume Viewer, it reverted back to "mesh" since that was the chosen volume style.
So if you really want to be able to adjust the level and keep it different style from the other level, I believe you would need to open the dataset twice and treat it as if it were two different datasets.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 4, 2020, at 7:44 AM, Guillaume Gaullier guillaume@gaullier.org wrote:
Hi Daniel,
Yes, I just tried, and saw it’s possible to display both with distinct styles and colors. In the volume viewer, the style and color options will only apply to the threshold cursor you moved or clicked last. I did not pay close attention to what the log reported when I tried, but it printed commands, so there is definitely a way to achieve the same thing with commands.
I hope this helps,
Guillaume
On 4 Dec 2020, at 15:08, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Hi Elaine,
Thank you for pointing out that if one right-clicks in the histogram of the volume in the volume viewer window, one can add a level. It was also easy to add another surface by giving multiple level arguments to the volume command.
Is it possible to show one contour as surface and one as mesh?
Regards, Daniel
On 2020-11-19, at 17:17, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Yes, often more than one isosurface is shown for a given map, and besides or as an alternative to making the outer one transparent, you can use the mesh style. The Volume Viewer tool's context menu (shown with right-click, except on Mac Ctrl-click) includes choices to add or delete thresholds, i.e. contour levels. http://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
Or it can be done with commands, as in the first example in the "volume" command documentation: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html
volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2020, at 12:35 AM, Daniel Larsson daniel.larsson@icm.uu.se wrote:
Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. 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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (4)
-
Daniel Larsson -
Elaine Meng -
Guillaume Gaullier -
Tom Goddard