Next/previous buttons?
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?
Hi Oli! To answer the PS: In ChimeraX you can assign function keys to execute commands, see "functionkey":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?
Oh wow, thanks Elaine, very nice!! with modifiers, too! And looking at that page I see there is also the capacity to make custom mousemode assignments, with keyboard modifiers, excellent! Does the functionkey command also understand aliases, I guess yes...?
Cheers Oli
On Sep 29, 2021, at 2:05 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli! To answer the PS: In ChimeraX you can assign function keys to execute commands, see "functionkey":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?
Hi Oli,
Yes, "functionkey" also works with aliases.
Elaine
On Sep 29, 2021, at 11:09 AM, Oliver Clarke olibclarke@gmail.com wrote:
Oh wow, thanks Elaine, very nice!! with modifiers, too! And looking at that page I see there is also the capacity to make custom mousemode assignments, with keyboard modifiers, excellent! Does the functionkey command also understand aliases, I guess yes...?
Cheers Oli
On Sep 29, 2021, at 2:05 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli! To answer the PS: In ChimeraX you can assign function keys to execute commands, see "functionkey":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Ah that is great, thanks Tom!
On Sep 29, 2021, at 3:30 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users 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, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
On Feb 2, 2022, at 2:11 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard goddard@sonic.net wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier guillaume.gaullier@icm.uu.se wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: > > Hi Oli, > > The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, > > mseries slider #1-5,7-12 > > allows displaying one of the specified models without effecting the display of models that are not listed in the command. > > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html > > Tom > > > >> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi, >> >> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >> >> Cheers >> Oli >> >> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >> <PastedGraphic-1.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
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It can't handle 50 maps - I wish it could - but it handles 20 just fine on a macbook screen. It is very useful for comparing many maps. Tiling is useful for comparing gross conformational changes, but for looking at subtle changes there s nothing better than quickly cycling between the different maps, comparing to a fixed "reference" map or model, in my opinion.
Oli
On Feb 2, 2022, at 3:58 PM, Tom Goddard goddard@sonic.net wrote:
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: > > I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). > > It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. > > Cheers > Oli > >> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >> >> Hi Oli, >> >> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >> >> mseries slider #1-5,7-12 >> >> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >> >> Tom >> >> >> >>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>> >>> Hi, >>> >>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>> >>> Cheers >>> Oli >>> >>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>> <PastedGraphic-1.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier guillaume.gaullier@icm.uu.se wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard goddard@sonic.net wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users > chimerax-users@cgl.ucsf.edu wrote: > > I've played with this a bit now Tom and I still think the > Chimera implementation is superior for some use cases, as it is > more flexible - it is easy to remove or add volumes or models to > the series "on the fly", whereas in ChimeraX this needs to be > done when creating the series (unless I am missing something > which is entirely possible!). > > It would be great to have at some point an implementation of a > "default" model/volume series as exists in Chimera, where one > can click next/prev or have an option to temporarily add/remove > each model from the series. > > Cheers > Oli > >> On Sep 29, 2021, at 3:30 PM, Tom Goddard goddard@sonic.net wrote: >> >> Hi Oli, >> >> The "mseries slider" command in ChimeraX provides a related >> capability to flip through several models using a slider, for >> example, >> >> mseries slider #1-5,7-12 >> >> allows displaying one of the specified models without effecting >> the display of models that are not listed in the command. >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >> >> Tom >> >> >> >>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users >>> chimerax-users@cgl.ucsf.edu wrote: >>> >>> Hi, >>> >>> The Next/Previous buttons in original Chimera, combined with >>> the capacity to lock the display status of one model (using >>> the "Skip") checkboxes, are really useful when comparing >>> multiple maps (particularly multiple aligned maps with a >>> single atomic model), and I really miss this functionality in >>> ChimeraX... would it be possible to add it to the >>> (diminishing!) list of features to port over? >>> >>> Cheers >>> Oli >>> >>> PS My mind was blown yesterday when I found out that ChimeraX >>> has (universal?) undo/redo bound to hotkeys! Would it be >>> possible to add the option of user defined hotkeys...? E.g. >>> for invoking a custom function, style, lighting etc? >>> <PastedGraphic-1.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
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Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal vincent.chaptal@ibcp.fr wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: > > Hi Oliver, > > You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. > > Tom > >> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >> >> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >> >> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >> >> Cheers >> Oli >> >>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>> >>> Hi Oli, >>> >>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>> >>> mseries slider #1-5,7-12 >>> >>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>> >>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>> >>> Tom >>> >>> >>> >>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>> >>>> Hi, >>>> >>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>> >>>> Cheers >>>> Oli >>>> >>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>> <PastedGraphic-1.png> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
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Hi Tom - yes, it is exactly that kind of fast flipping between subsets of classes that is useful, often while rotating the model and looking at it from different directions. This already works well in Chimera - if it would help I can make a screen recording of how it works in Chimera, if that is helpful?
Cheers Oli
On Feb 3, 2022, at 5:56 PM, Tom Goddard goddard@sonic.net wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.fr mailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: > > Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. > > So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another. > > Cheers > Oli > > <PastedGraphic-1.png> > >> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >> >> Hi Oliver, >> >> You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. >> >> Tom >> >>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>> >>> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >>> >>> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >>> >>> Cheers >>> Oli >>> >>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>> >>>> Hi Oli, >>>> >>>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>>> >>>> mseries slider #1-5,7-12 >>>> >>>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>>> >>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>>> >>>> Tom >>>> >>>> >>>> >>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>> >>>>> Hi, >>>>> >>>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>>> >>>>> Cheers >>>>> Oli >>>>> >>>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>>> <PastedGraphic-1.png> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list >>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>> Manage subscription: >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/ http://mmsb.cnrs.fr/en/
Hi Oliver,
Yes a screen recording would give a much clearer sense of what you are doing.
Tom
On Feb 3, 2022, at 3:07 PM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom - yes, it is exactly that kind of fast flipping between subsets of classes that is useful, often while rotating the model and looking at it from different directions. This already works well in Chimera - if it would help I can make a screen recording of how it works in Chimera, if that is helpful?
Cheers Oli
On Feb 3, 2022, at 5:56 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.fr mailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
> On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: > > Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin. > > Tom > > >> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. >> >> So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another. >> >> Cheers >> Oli >> >> <PastedGraphic-1.png> >> >>> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>> >>> Hi Oliver, >>> >>> You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. >>> >>> Tom >>> >>>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>> >>>> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >>>> >>>> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >>>> >>>> Cheers >>>> Oli >>>> >>>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>>> >>>>> Hi Oli, >>>>> >>>>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>>>> >>>>> mseries slider #1-5,7-12 >>>>> >>>>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>>>> >>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>>>> >>>>> Tom >>>>> >>>>> >>>>> >>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>>>> >>>>>> Cheers >>>>>> Oli >>>>>> >>>>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>>>> <PastedGraphic-1.png> >>>>>> _______________________________________________ >>>>>> ChimeraX-users mailing list >>>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>>> Manage subscription: >>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
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MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/ http://mmsb.cnrs.fr/en/
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Sorry, I sent my previous answer before I finished reading the discussion. My use case is mostly to compare many maps that are already aligned (or already close enough that I don’t need to align them anyway), and I need to be able to do things like:
1. scroll through all maps (vseries does this very well, with the slider or play button if I want to let it cycle through the series), 2. keep any number of maps with arbitrary indices displayed, while scrolling through all other maps, 3. display any number of maps with arbitrary indices while hiding all the others
1 is easy to do with vseries. 2 and 3 are doable with the model panel checkboxes, but are tedious and clicking-intensive beyond about 10 maps (and typical work easily gets you 50 maps to look at) since you need to uncheck map n and check map n+1 every time you want to show the next map. 3 is doable with a command, so I should study the model selection syntax more closely and stop complaining. But I can’t see how to do 2 with a command.
So everything I need to do is doable with ChimeraX in its current form, but if some of these things required less clicks I would not shy away from looking at more than 50 maps.
I hope this description helps understanding the use case. Curious to see the screen recording from Oli. Cheers,
Guillaume
On 3 Feb 2022, at 23:56, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.frmailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit : Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.semailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.frhttp://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/
Hi all,
Here is a quick screen recording:
https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=... https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=0
This is a mock up, so there's not much interesting to see, but in this case I am comparing different maps from the output of a 3D classification run with an atomic model. The interface in chimera allows me to easily and quickly compare all the classes to both each other and to the atomic model, identify the good ones and then compare those, while deselecting the others, quickly flick between just two classes, and then to compare two classes with a fixed third class.
Currently I find it hard to do anything like this in ChimeraX, but it may be just that I haven't spent enough time with it.
In "real" examples I would be looking for subtle conformational differences (or perhaps the presence/absence of a ligand/ion/water at higher resolution) between the classes, which flicking quickly between maps can help discern, but there is not much to see on that front here - does this recording make it easier to understand the use case?
Cheers Oli
On Feb 7, 2022, at 8:42 AM, Guillaume Gaullier guillaume.gaullier@icm.uu.se wrote:
Sorry, I sent my previous answer before I finished reading the discussion. My use case is mostly to compare many maps that are already aligned (or already close enough that I don’t need to align them anyway), and I need to be able to do things like:
- scroll through all maps (vseries does this very well, with the slider or play button if I want to let it cycle through the series),
- keep any number of maps with arbitrary indices displayed, while scrolling through all other maps,
- display any number of maps with arbitrary indices while hiding all the others
1 is easy to do with vseries. 2 and 3 are doable with the model panel checkboxes, but are tedious and clicking-intensive beyond about 10 maps (and typical work easily gets you 50 maps to look at) since you need to uncheck map n and check map n+1 every time you want to show the next map. 3 is doable with a command, so I should study the model selection syntax more closely and stop complaining. But I can’t see how to do 2 with a command.
So everything I need to do is doable with ChimeraX in its current form, but if some of these things required less clicks I would not shy away from looking at more than 50 maps.
I hope this description helps understanding the use case. Curious to see the screen recording from Oli. Cheers,
Guillaume
On 3 Feb 2022, at 23:56, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.fr mailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
> On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: > > Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin. > > Tom > > >> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. >> >> So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another. >> >> Cheers >> Oli >> >> <PastedGraphic-1.png> >> >>> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>> >>> Hi Oliver, >>> >>> You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. >>> >>> Tom >>> >>>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>> >>>> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >>>> >>>> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >>>> >>>> Cheers >>>> Oli >>>> >>>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>>> >>>>> Hi Oli, >>>>> >>>>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>>>> >>>>> mseries slider #1-5,7-12 >>>>> >>>>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>>>> >>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>>>> >>>>> Tom >>>>> >>>>> >>>>> >>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>>>> >>>>>> Cheers >>>>>> Oli >>>>>> >>>>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>>>> <PastedGraphic-1.png> >>>>>> _______________________________________________ >>>>>> ChimeraX-users mailing list >>>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>>> Manage subscription: >>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/ http://mmsb.cnrs.fr/en/
To be clear I'm not saying this is the optimal interface - I agree with Tom that rows of checkboxes are cumbersome - I just want the flexibility and rapid switching afforded by this interface (however it is implemented). Capacity to deal with even more maps/models would be great!
Cheers Oli
On Feb 7, 2022, at 9:20 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi all,
Here is a quick screen recording:
https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=... https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=0
This is a mock up, so there's not much interesting to see, but in this case I am comparing different maps from the output of a 3D classification run with an atomic model. The interface in chimera allows me to easily and quickly compare all the classes to both each other and to the atomic model, identify the good ones and then compare those, while deselecting the others, quickly flick between just two classes, and then to compare two classes with a fixed third class.
Currently I find it hard to do anything like this in ChimeraX, but it may be just that I haven't spent enough time with it.
In "real" examples I would be looking for subtle conformational differences (or perhaps the presence/absence of a ligand/ion/water at higher resolution) between the classes, which flicking quickly between maps can help discern, but there is not much to see on that front here - does this recording make it easier to understand the use case?
Cheers Oli
On Feb 7, 2022, at 8:42 AM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Sorry, I sent my previous answer before I finished reading the discussion. My use case is mostly to compare many maps that are already aligned (or already close enough that I don’t need to align them anyway), and I need to be able to do things like:
- scroll through all maps (vseries does this very well, with the slider or play button if I want to let it cycle through the series),
- keep any number of maps with arbitrary indices displayed, while scrolling through all other maps,
- display any number of maps with arbitrary indices while hiding all the others
1 is easy to do with vseries. 2 and 3 are doable with the model panel checkboxes, but are tedious and clicking-intensive beyond about 10 maps (and typical work easily gets you 50 maps to look at) since you need to uncheck map n and check map n+1 every time you want to show the next map. 3 is doable with a command, so I should study the model selection syntax more closely and stop complaining. But I can’t see how to do 2 with a command.
So everything I need to do is doable with ChimeraX in its current form, but if some of these things required less clicks I would not shy away from looking at more than 50 maps.
I hope this description helps understanding the use case. Curious to see the screen recording from Oli. Cheers,
Guillaume
On 3 Feb 2022, at 23:56, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.fr mailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
> On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: > > Hi Tom, > > It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :) > > Cheers > Oli > >> On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >> >> Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin. >> >> Tom >> >> >>> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>> >>> Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. >>> >>> So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another. >>> >>> Cheers >>> Oli >>> >>> <PastedGraphic-1.png> >>> >>>> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>> >>>> Hi Oliver, >>>> >>>> You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. >>>> >>>> Tom >>>> >>>>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>> >>>>> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >>>>> >>>>> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >>>>> >>>>> Cheers >>>>> Oli >>>>> >>>>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>>>> >>>>>> Hi Oli, >>>>>> >>>>>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>>>>> >>>>>> mseries slider #1-5,7-12 >>>>>> >>>>>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>>>>> >>>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>>>>> >>>>>> Tom >>>>>> >>>>>> >>>>>> >>>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>>>>> >>>>>>> Cheers >>>>>>> Oli >>>>>>> >>>>>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>>>>> <PastedGraphic-1.png> >>>>>>> _______________________________________________ >>>>>>> ChimeraX-users mailing list >>>>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>>>> Manage subscription: >>>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>>> >>>>> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list >>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>> Manage subscription: >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/ http://mmsb.cnrs.fr/en/
Hi Oliver, Guillaume
Video and description of the 3 capabilities was very helpful. I made a ChimeraX feature request to discuss this further
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6106
since I think it is too much detail for most of the mailing list participants.
Tom
On Feb 7, 2022, at 6:30 AM, Oliver Clarke olibclarke@gmail.com wrote:
To be clear I'm not saying this is the optimal interface - I agree with Tom that rows of checkboxes are cumbersome - I just want the flexibility and rapid switching afforded by this interface (however it is implemented). Capacity to deal with even more maps/models would be great!
Cheers Oli
On Feb 7, 2022, at 9:20 AM, Oliver Clarke <olibclarke@gmail.com mailto:olibclarke@gmail.com> wrote:
Hi all,
Here is a quick screen recording:
https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=... https://www.dropbox.com/s/jlbhbjqy9mdrb74/screen_recording_next_prev.mov?dl=0
This is a mock up, so there's not much interesting to see, but in this case I am comparing different maps from the output of a 3D classification run with an atomic model. The interface in chimera allows me to easily and quickly compare all the classes to both each other and to the atomic model, identify the good ones and then compare those, while deselecting the others, quickly flick between just two classes, and then to compare two classes with a fixed third class.
Currently I find it hard to do anything like this in ChimeraX, but it may be just that I haven't spent enough time with it.
In "real" examples I would be looking for subtle conformational differences (or perhaps the presence/absence of a ligand/ion/water at higher resolution) between the classes, which flicking quickly between maps can help discern, but there is not much to see on that front here - does this recording make it easier to understand the use case?
Cheers Oli
On Feb 7, 2022, at 8:42 AM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote:
Sorry, I sent my previous answer before I finished reading the discussion. My use case is mostly to compare many maps that are already aligned (or already close enough that I don’t need to align them anyway), and I need to be able to do things like:
- scroll through all maps (vseries does this very well, with the slider or play button if I want to let it cycle through the series),
- keep any number of maps with arbitrary indices displayed, while scrolling through all other maps,
- display any number of maps with arbitrary indices while hiding all the others
1 is easy to do with vseries. 2 and 3 are doable with the model panel checkboxes, but are tedious and clicking-intensive beyond about 10 maps (and typical work easily gets you 50 maps to look at) since you need to uncheck map n and check map n+1 every time you want to show the next map. 3 is doable with a command, so I should study the model selection syntax more closely and stop complaining. But I can’t see how to do 2 with a command.
So everything I need to do is doable with ChimeraX in its current form, but if some of these things required less clicks I would not shy away from looking at more than 50 maps.
I hope this description helps understanding the use case. Curious to see the screen recording from Oli. Cheers,
Guillaume
On 3 Feb 2022, at 23:56, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Vincent,
I'm glad to hear from all of you about this need. I get how mseries or the Chimera next/prev/skip buttons allows you flip through maps or class average images. Oliver wants some finer control than mseries allows and the Chimera user interface is cumbersome (rows of checkbuttons for every model) and I am missing the fine details of how the comparisons are done in practice that would allow an improved capability. For instance astronomers will quickly flip back and forth between two perfectly aligned images of the sky to see if anything changed (e.g. a supernova) -- the comparison requires fast aligned flipping repeated many times. I don't understand the precise kinds of comparisons you, Guillaume and Oliver are talking about, so it is hard to develop anything to help.
Tom
On Feb 3, 2022, at 12:20 AM, vincent Chaptal <vincent.chaptal@ibcp.fr mailto:vincent.chaptal@ibcp.fr> wrote:
Hi,
we use the mseries a lot to compare maps and create movies. It is really great and allows for preliminary observations. Now that we are now moving in more detailed examinations, I can see where Oliver's query goes and is interesting. I also think it's not a niche but the future of cryoEM observations.
More tools along these lines could only be an asset. Best Vincent
Le 02/02/2022 à 21:58, Tom Goddard via ChimeraX-users a écrit :
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
> On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.se mailto:guillaume.gaullier@icm.uu.se> wrote: > > Hi, > > Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help! > > Cheers, > > Guillaume > > >> On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi Tom, >> >> It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :) >> >> Cheers >> Oli >> >>> On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>> >>> Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin. >>> >>> Tom >>> >>> >>>> On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>> >>>> Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence. >>>> >>>> So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another. >>>> >>>> Cheers >>>> Oli >>>> >>>> <PastedGraphic-1.png> >>>> >>>>> On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>>> >>>>> Hi Oliver, >>>>> >>>>> You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works. >>>>> >>>>> Tom >>>>> >>>>>> On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>>> >>>>>> I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!). >>>>>> >>>>>> It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series. >>>>>> >>>>>> Cheers >>>>>> Oli >>>>>> >>>>>>> On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: >>>>>>> >>>>>>> Hi Oli, >>>>>>> >>>>>>> The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example, >>>>>>> >>>>>>> mseries slider #1-5,7-12 >>>>>>> >>>>>>> allows displaying one of the specified models without effecting the display of models that are not listed in the command. >>>>>>> >>>>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html >>>>>>> >>>>>>> Tom >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? >>>>>>>> >>>>>>>> Cheers >>>>>>>> Oli >>>>>>>> >>>>>>>> PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? >>>>>>>> <PastedGraphic-1.png> >>>>>>>> _______________________________________________ >>>>>>>> ChimeraX-users mailing list >>>>>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>>>>> Manage subscription: >>>>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> ChimeraX-users mailing list >>>>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>>>> Manage subscription: >>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > > > > > > > > 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/ 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 http://www.uu.se/en/about-uu/data-protection-policy
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-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://www.appicom.cnrs.fr/ http://mmsb.cnrs.fr/en/ http://mmsb.cnrs.fr/en/
Hi Tom,
Sorry for this late answer, I got swamped by other things recently.
I have not used this feature because I have been trying to only use ChimeraX. But from Oli’s description I can tell that comparing many maps is a use case I have encountered too. So far, I have only done so with the "display" checkboxes in the model panel in ChimeraX, but this can quickly get tedious since you need two clicks to do "next map" (one click to hide map n, another click to display map n+1). I have used the volume series feature, and for certain types of work it is perfect. But it does not help much when all your maps are a random sample from a distribution and are not related by any sequential order, and you want to compare arbitrarily (in a volume series, you can jump to an arbitrary index with a command, but the GUI doesn’t make this very easy).
Cheers,
Guillaume
On 2 Feb 2022, at 21:58, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Guillaume,
The row of checkbuttons (default 10 buttons one for each model) will not handle 50 maps unless you have an extremely wide screen (about two normal screens wide) with Chimera shown full width. I don't understand how it is useful for comparing many maps since I have not used it. Of course often we have dozens of data sets open and compare them. For example the tile command can show them all in a rectangular grid, and there are many many other ways.
Have you used the Chimera "displayed models" and "skip models" check buttons below the command-line?
Tom
On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier <guillaume.gaullier@icm.uu.semailto:guillaume.gaullier@icm.uu.se> wrote:
Hi,
Just to confirm that this is also my experience with cryoEM. For very straightforward projects, you can get away with only a handful of maps (I typically request 4 from normal 3D classification). But once you’re using advanced methods to analyze heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is very common to have to examine 50 maps or more every time you get results from a new job, and you rarely run a single job. Having more ways to navigate multiple maps can only help!
Cheers,
Guillaume
On 2 Feb 2022, at 20:37, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
It is increasingly not niche at least for single particle cryo-EM folks - pretty much all of us deal with the issue of comparing many classes, or sets of classes, in the context of one or more atomic models. Anything that facilitates that is useful to most of us in the field these days in my experience. Believe me if I had the faintest idea how to add it in I would do so! :)
Cheers Oli
On Feb 2, 2022, at 2:34 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Got it. Never knew about that "skip in previous/next" row in the Chimera daily build. Seems really like a niche feature but I understand it is useful to you. This is the kind of feature that is so special purpose that it would be good candidate for someone who really benefits from it to implement it as a ChimeraX plugin.
Tom
On Feb 2, 2022, at 11:20 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, right - in recent-ish nightly builds of Chimera Eric added another row - "skip in previous/next" which allows one to control which models are excluded from the sequence.
So in the attached picture, models 3&4 would be excluded from the sequence - #3 would always be displayed, while #4 would always be hidden. This is very useful to be able to do on the fly, when one is comparing lots of different models & 3D classes that are aligned to one another.
Cheers Oli
<PastedGraphic-1.png>
On Feb 2, 2022, at 2:11 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oliver,
You are right the ChimeraX mseries command does not allow you to easily remove or add models to the sequence if models that the slider displays. Could you explain how that works in Chimera? I guess you are referring to the optional row of "Displayed model" checkbuttons below the command line in Chimera that can be shown using command-line preferences and has Next and Previous buttons. But I don't understand how that lets you change which models you cycle through -- doesn't it always cycle through all models in model number order? Eric implemented that Chimera feature and maybe I just don't understand how it works.
Tom
On Feb 2, 2022, at 8:43 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
I've played with this a bit now Tom and I still think the Chimera implementation is superior for some use cases, as it is more flexible - it is easy to remove or add volumes or models to the series "on the fly", whereas in ChimeraX this needs to be done when creating the series (unless I am missing something which is entirely possible!).
It would be great to have at some point an implementation of a "default" model/volume series as exists in Chimera, where one can click next/prev or have an option to temporarily add/remove each model from the series.
Cheers Oli
On Sep 29, 2021, at 3:30 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:
Hi Oli,
The "mseries slider" command in ChimeraX provides a related capability to flip through several models using a slider, for example,
mseries slider #1-5,7-12
allows displaying one of the specified models without effecting the display of models that are not listed in the command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html
Tom
On Sep 29, 2021, at 9:42 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over?
Cheers Oli
PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc? <PastedGraphic-1.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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participants (5)
-
Elaine Meng -
Guillaume Gaullier -
Oliver Clarke -
Tom Goddard -
vincent Chaptal