[chimerax-users] ChimeraX VR question or suggestions

[Tom Goddard]

Hi Alejandro,

  You can assign mouse modes to VR hand controller buttons.  For example, this ChimeraX command, makes the right grip button toggle the selection of the segmented region you are pointing at

	vr button grip "select toggle" hand right

Here is the vr button command documentation

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/device.html#vr-button <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/device.html#vr-button>

and the documentation for mouse modes

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/ui.html#functions <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>

The Segment Map tool has no corresponding command to do most of the operations the user interface panel does, so unfortunately you can't use a command to write out the regions you want.  But you can use the user interface panel.  This Segment Map (also known as Segger) tool was written by Greg Pintilie and I think he still works on the old Chimera, and not ChimeraX.

  Tom

> On Dec 14, 2021, at 6:26 AM, Alejandro Villalta via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Tom,
> 
> I was talking about electronic microscopy maps. I did a segmentation of the map and then I wanted to select only the regions that were of interest to me. I tried to hold the selection button  but it select all the regions. Nevertheless I didn't try to hold while pressing another button. with the button down do you mean the joystick pointing toward down? I used a Quest2. I don't know if it can help but intuitively, I tried to press the grip spectating that that could work as shift. I tried to remove the headset and select with the mouse on the flat screen but it didn't allow me to click. I also tried to select on VR while pressing the shift button on the keyboard and didn't work.
> 
> Yes, I understand that the command lines on VR could be not easy, nothing as a keyboard to write. But what I meant is that if you know the name of the regions you could select them on after the flatscreen by command lines. 
> 
> Thank you very much for your reply
> 
> Alejandro
> 
> On 12/13/21 7:34 PM, Tom Goddard wrote:
>> Hi Alejandro,
>> 
>>   Thanks for your VR suggestions!
>> 
>>   When you say segment or select different segments do you mean atomic models or are you talking about electron microscopy maps?  I guess you mean selecting parts of an atomic model.  Using the VR hand controller with a button assigned to the "select" mode you can point at an atom or ribbon residue and select it.  If you hold the button down and then move your hand upward when selecting it will extend the selection to select the whole residue, whole helix, beta strand, or turn, whole chain.  With a mouse you can select multiple parts by holding the shift key, but we don't have an equivalent for that in VR.  Can you tell me what you were trying to select so I can think about how it could be done with the VR hand controller.
>> 
>>   I agree that it would be nice if pointing the VR controller at an atom could show the chain id, residue number, and atom name in a popup.  Since you can't currently type commands in VR it would not be so useful for commands, but it is could to be able to figure out which residues you are looking at.  I have not added a virtual VR keyboard because it is excruciatingly slow to type commands by poking with VR controllers.  There are a lot of challenges to make the VR user interface work well.  It makes you appreciate how powerful the mouse and keyboard are when you are reduced to using hand controllers with a few buttons.
>> 
>> 	Tom
>> 
>> 
>>> On Dec 13, 2021, at 8:44 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>>> 
>>>> From: Alejandro Villalta Cásares <alejandrovillaltac at gmail.com <mailto:alejandrovillaltac at gmail.com>>
>>>> Subject: ChimeraX VR question or suggestions
>>>> Date: December 13, 2021 at 4:36:03 AM PST
>>>> To: chimerax at cgl.ucsf.edu <mailto:chimerax at cgl.ucsf.edu>
>>>> 
>>>> Dear ChimeraX staff,
>>>> 
>>>> I tested the ChimeraX VR mode today. I was very happy on how it looks and how easy it was to move and see some parts of the structure compared to the flat screen version. Nevertheless, the function that I think it will very useful the VR is to segment and select different segments to save them later. That I couldn't manage to do it after some time I managed to be able to select one region but no more than one at time. It should be nice to add the ability to select multiple regions or at least as in the flat screen that it tells you the name of the models that you are pointing, like that we could pass through command lines. Also it should be nice that a keyboard appears on the headset in order to type on the command lines, but it is true that is a minor point, if it can be written directly on the PC.
>>>> 
>>>> Thank you very much for this amazing function,
>>>> 
>>>> I hope that this constructive mail could help you to improve it more.
>>>> 
>>>> Sincerely yours,
>>>> 
>>>> Alejandro Villalta
>>>> 
>>> 
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