mousemode alt right contour
mousemode right clip
mousemode alt left "translate selected models"
mousemode shift left "rotate selected models”
Which works out to:
Alt/option-right-drag adjusts map threshold
Alt/option-right-drag moves the front screen clip plane
Shift+alt/option-right-drag moves both screen clip planes
Alt/option-left-drag translates selected model(s)
Shift+alt/option-left-drag rotates selected model(s)
And then trackpad gestures for general rotation/translation/zoom.
I think that covers the most commonly used ones without too many conflicts..
The only thing that would be nice would be if ChimeraX right mouse modes reverted to the startup settings after using one of the ones in the GUI. What I mean is, if these buttons were modal, which seems to almost be the case:
* When I initially start ChimeraX, none of the right mouse mode buttons in the “Right Mouse” toolbar are highlighted, and the settings I have defined in the startup script behave as expected.
* If I click a right mouse mode, that mode is enabled, and the relevant icon is highlighted in green.
* However if I click it again, the mode remains the same - there is no obvious way to revert to the custom right mouse mode defined in startup.
* It would be nice if a second click on the icon reverted the right mouse mode to the default, or if there was a “reset” mouse mode that reverted to the mode defined at startup.
Cheers
Oli
On Sep 8, 2023, at 5:59 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
All this flexibility with how shift/ctrl/alt interact with mouse modes is tripping you up. When you assign shift-left-mouse to do "rotate selected models" you need to understand that that mouse mode has its own special handling of the shift key, so if shift is pressed when in "rotate selected models" mode then it does a translation. So you'll find if you use shift-left to get into that rotation mode it does a translation because you have the shift key held down, and if you release the shift key while keeping the mouse button pressed it will start rotating!
The trouble here is if you both have the shift/ctrl/alt keys assigned to different mouse modes, and also have those mouse modes do special things when shift/ctrl/alt are held down, you are likely to confuse yourself. So choose your poison. I would suggest not binding rotation/translation modes to shift-mouse-button or ctrl-mouse-button to avoid confusion.
What we are up against here is that you want to use 10 different mouse behaviors but you only have at most 3 buttons (or maybe 1 button when using a trackpad). The modifier keys can only remedy this a little bit.
Tom
On Sep 8, 2023, at 2:20 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Ok, so I have it set up better now, but there is still something I don’t understand. I have the following mouse mode settings in my startup:
mousemode alt left "translate selected models"
mousemode shift left "rotate selected models”
I would expect that alt/option-left-click-drag would translate the selected model(s), while shift-left-click-drag would rotate the selected models.
However, shift-left-click-drag still translates the selected model - but shift-alt/option-left-click-drag rotates it! Is this the expected behavior?
Cheers
Oli
On Sep 8, 2023, at 5:10 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Ah… I was using “move picked models”… I guess this is different from “move selected models”… got it… thanks!!
On Sep 8, 2023, at 5:07 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oli,
Ok, I see you mean the trackpad multi-finger gestures are more ergonomic than holding buttons down on a mouse or trackpad. Currently I don't think the ChimeraX trackpad modes can be changed although we have discussed that and Tristan added Python support for it that I think ISOLDE uses.
To move 4 atomic models into a map as a group in ChimeraX you would use the move model mouse mode which moves just the selected models, select the 4 models, then move them. You would not need to move them one at a time, and there is no risk of accidentally moving the map. You are probably thinking of the "Drag Model" mouse mode which moves what you click on.
Tom
On Sep 8, 2023, at 1:54 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
Thanks for the suggestions! As usual you have good ideas, and as usual I don't completely understand them!
:)
Did you know one of the very nice features of ChimeraX for moving by hand an atomic model into a map is that if you press the shift key while doing a mouse rotation it switches to translation, and pressing shift in the translation mouse mode does a rotation? So by just pressing and releasing the shift key as you move the model around you can both translate and rotate.
I do know this, and agree it is convenient. I do find trackpad gestures in Chimera more ergonomic still, because once the appropriate sets of molecules are activated/deactivated, one doesn’t have to press down on the trackpad, click on any particular molecule, or press a modifier key - it is just a matter of switching between lightly swiping with two fingers (rotation) and three fingers (translation) (plus ctrl-right-click-drag for z-translation). This doesn’t matter so much to functionality I guess, but I find it strains my hands less when doing it a lot.
The secondary reason (perhaps more important) why I would like the capacity to lock (/deactivate) atomic models/maps is that it adds more flexibility and precision.
Consider the following situation:
1. I have a group of five (aligned) structures I want to fit to a single map (and I do not want to move the map, as I want to save the structures with respect to the map for opening in other software). In Chimera, I would deactivate the map, rotate/translate all models at once to approximately fit, then reactivate the map and fit all the models using fitmap. In ChimeraX, I would have to move the models one by one, and take care not to accidentally drag the map around (as the control of which model I move depends on what I click on in the window - this is particularly an issue if the model is partially obscured by the map).
Both approaches have their advantages and disadvantages, but having the option of locking/deactivating models/maps would definitely offer more flexibility I think.
I’m not sure I exactly explained it, but I hope that makes it a tad clearer?
Cheers and thanks for your patience as always,
Oli
On Sep 8, 2023, at 7:30 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One of the other advantages of this (locking a model) is that it also allows for repositioning of other models in the z direction - z translation of models in ChimeraX is (I think?) not possible, and in Chimera z translation was very convenient, allowing quick repositioning of a model into a map with a couple of quick motions
On Sep 8, 2023, at 9:52 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Alternatively, a unique keyboard modifier (e.g. Shift-Ctrl) that if applied to all gestures allowed trackpad rotation/translation of the selected model would also accomplish the same thing, but not sure if this is possible...
On Sep 8, 2023, at 9:48 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
I know that in ChimeraX the preferred way to manipulate models with respect to one another is using the mouse modes.
This works, but is still (in my experience) less precise/ergonomic than deactivating selected models in Chimera and freely manipulating the remaining active models using the trackpad/mouse.
Is there any possibility in the future (or present) of adding the capacity to “lock" selected models to rotation/translation, to allow free manipulation of the remainder?
Cheers
Oli
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