Feature request regarding clipping planes
Hi Team, Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion. If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Sorry for the confusing description, I was alluding to the first scenario. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Mon, Nov 15, 2021 at 4:04 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map. Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Oooh! That too, btw, I really like Chimera's ability push/pull the model/surface towards or away from the user. Currently it seems the selected has only 2˚ of translational freedom... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Mon, Nov 15, 2021 at 4:18 PM Oliver Clarke <olibclarke@gmail.com> wrote:
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map.
Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Yes seconded! A "Translate-Z" right mouse mode would be really useful Cheers Oli
On Nov 15, 2021, at 11:20 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Oooh! That too, btw, I really like Chimera's ability push/pull the model/surface towards or away from the user. Currently it seems the selected has only 2˚ of translational freedom... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Nov 15, 2021 at 4:18 PM Oliver Clarke <olibclarke@gmail.com> wrote:
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map.
Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Pranav, Oli, Could you explain the translate-Z mouse mode you want a bit more? Do you mean you want to move just the selected model in z while other models do not move? Or do you mean you want to move all models in z relative to the clip planes (already possible by moving the two clip planes together)? And there is a "move selected atoms" mouse mode, do you want that to be able to move in z? Currently when you are in any of the move modes if you hold the shift key down it switches from xy translation to rotation. This makes it quick to switch between translating and rotating and back just using the shift key. But there is no trick to translate in z. Actually if you have a mouse wheel, then you can assign it to translate and it will do a z translation (command: mouse wheel "translate selected models"). Tom
On Nov 15, 2021, at 9:10 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Yes seconded! A "Translate-Z" right mouse mode would be really useful
Cheers Oli
On Nov 15, 2021, at 11:20 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Oooh! That too, btw, I really like Chimera's ability push/pull the model/surface towards or away from the user. Currently it seems the selected has only 2˚ of translational freedom... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Nov 15, 2021 at 4:18 PM Oliver Clarke <olibclarke@gmail.com> wrote:
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map.
Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, The first one - move in Z relative to other models. This is useful when fitting a model to a map, it is possible in Chimera but not in ChimeraX I think? Cheers Oli
On Nov 15, 2021, at 5:39 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav, Oli,
Could you explain the translate-Z mouse mode you want a bit more? Do you mean you want to move just the selected model in z while other models do not move? Or do you mean you want to move all models in z relative to the clip planes (already possible by moving the two clip planes together)? And there is a "move selected atoms" mouse mode, do you want that to be able to move in z?
Currently when you are in any of the move modes if you hold the shift key down it switches from xy translation to rotation. This makes it quick to switch between translating and rotating and back just using the shift key. But there is no trick to translate in z. Actually if you have a mouse wheel, then you can assign it to translate and it will do a z translation (command: mouse wheel "translate selected models").
Tom
On Nov 15, 2021, at 9:10 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Yes seconded! A "Translate-Z" right mouse mode would be really useful
Cheers Oli
On Nov 15, 2021, at 11:20 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Oooh! That too, btw, I really like Chimera's ability push/pull the model/surface towards or away from the user. Currently it seems the selected has only 2˚ of translational freedom... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Nov 15, 2021 at 4:18 PM Oliver Clarke <olibclarke@gmail.com> wrote:
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map.
Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, Gladly! What Oli and I were referring to was the ability to translate the selected object(s) in Z. In Chimera this is achieved by holding down ctrl+alt+rt.click and moving the mouse up to "push" the object further into the screen (or away from the viewer) or down to pull the object towards the viewer. RE clipping planes - I think holding down the middle-mouse button on the foreground clipping plane allows the user to display slabs of density and "scroll" through it in Z whereas the same operation when performed on the background clipping plane enables the user to choose the thickness of the represented slab. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Mon, Nov 15, 2021 at 10:39 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav, Oli,
Could you explain the translate-Z mouse mode you want a bit more? Do you mean you want to move just the selected model in z while other models do not move? Or do you mean you want to move all models in z relative to the clip planes (already possible by moving the two clip planes together)? And there is a "move selected atoms" mouse mode, do you want that to be able to move in z?
Currently when you are in any of the move modes if you hold the shift key down it switches from xy translation to rotation. This makes it quick to switch between translating and rotating and back just using the shift key. But there is no trick to translate in z. Actually if you have a mouse wheel, then you can assign it to translate and it will do a z translation (command: mouse wheel "translate selected models").
Tom
On Nov 15, 2021, at 9:10 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Yes seconded! A "Translate-Z" right mouse mode would be really useful
Cheers Oli
On Nov 15, 2021, at 11:20 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Oooh! That too, btw, I really like Chimera's ability push/pull the model/surface towards or away from the user. Currently it seems the selected has only 2˚ of translational freedom... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Mon, Nov 15, 2021 at 4:18 PM Oliver Clarke <olibclarke@gmail.com> wrote:
On the same topic, it would be useful to be able to switch the view side like one can in chimera (right v top). This is useful when trying to precisely orient a model/map.
Cheers Oli
On Nov 15, 2021, at 11:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean the vertical line in the Side View? You are right, they are very thin and hard to see especially on a high-resolution screen. Currently there is no user control -- thanks for the suggestion.
If you also meant the appearance in the main window, currently ChimeraX does not show the clipping plane at all. The transparent disc that is displayed during manipulation of a per-model clipping plane in Chimera is very useful, and I would like something like that myself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2021, at 2:49 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team,
Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image).
Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Oliver Clarke -
Pranav Shah -
Tom Goddard