Tile behavior in Chimera vs ChimeraX - different behavior of independent rotation?
Hi all,
Happy new year!
I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX.
In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line.
In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently).
Cheers Oli
Hi Oli, Happy new year to you too!
Request aside (I'll leave it to others to respond when they return to work), I note that you can rock a set of tiled models about their own centers with commands, but it is somewhat annoying if there is a large number of models.
E.g. if you had models #1-#4 tiled, then you could use something like the following, entered as a single line:
rock y model #1 center #1; rock y model #2 center #2; rock y model #3 center #3; rock y model #4 center #4
Similarly, roll and turn commands also have "center" options to get this kind of behavior.
If this was in a command file, I *think* it would be equivalent to just put one rock command per line since the ChimeraX behavior (unlike Chimera) is to go directly to the next command in a script without implicitly waiting a frame after each line. However, I personally get confused about this sometimes, and resort to experimentation to confirm.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 3, 2024, at 10:32 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Happy new year!
I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX.
In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line.
In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently).
Cheers Oli
Hi Oli,
Perhaps we can make the rock (and turn and roll) commands have an option to rotate each model about their own center. I've made a ChimeraX feature request for that
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10427
Here is why it doesn't work the same as in old Chimera if you are curious. ChimeraX and Chimera have a function that returns the center of rotation. In ChimeraX this is just single point and lots of code uses that. If I were to change it so the center of rotation can be different for each model, then every place in the code that uses center of rotation needs to handle this obscure feature in some way. While in Chimera we did that I'd say it was a mistake in terms of the cost in programmer time versus benefit to users. We want to spend our limited time working on code that lots of people will use, such as running AlphaFold structure predictions. Those won't get done if we are spending time implementing rarely used features that impact lots of code. I realize it is not obvious how much code has to be changed to support a feature like center of rotation that is not a single point in the scene.
Tom
On Jan 3, 2024, at 10:32 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Happy new year!
I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX.
In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line.
In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently).
Cheers Oli _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Makes sense, thanks Tom!!
Oli
On Jan 4, 2024, at 5:08 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
Perhaps we can make the rock (and turn and roll) commands have an option to rotate each model about their own center. I've made a ChimeraX feature request for that
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10427
Here is why it doesn't work the same as in old Chimera if you are curious. ChimeraX and Chimera have a function that returns the center of rotation. In ChimeraX this is just single point and lots of code uses that. If I were to change it so the center of rotation can be different for each model, then every place in the code that uses center of rotation needs to handle this obscure feature in some way. While in Chimera we did that I'd say it was a mistake in terms of the cost in programmer time versus benefit to users. We want to spend our limited time working on code that lots of people will use, such as running AlphaFold structure predictions. Those won't get done if we are spending time implementing rarely used features that impact lots of code. I realize it is not obvious how much code has to be changed to support a feature like center of rotation that is not a single point in the scene.
Tom
On Jan 3, 2024, at 10:32 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Happy new year!
I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX.
In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line.
In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently).
Cheers Oli _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Elaine Meng -
Oliver Clarke -
Tom Goddard