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Visualizing protein structures?

CountBorgula
Level 4
Has anyone gotten a biomolecular viewer working with the Oculus Rift yet? This was one of my primary motivations for getting this, and just wondering what work has already been done on this. Here are a couple of programs that this could be made to work with:

http://www.ks.uiuc.edu/Research/vmd/ (my favorite)

http://accelrys.com/resource-center/downloads/freeware/index.html

I can already view in 3D with VMD, by setting Stereo to side by side, but there is no distortion and I don't know how to get the headtracker to work.

CountBorgula
20 REPLIES 20

albymassa
Level 2
Hi
There is anyone tried IMV? Most of the website (Downloads/Screenshots/Contacts pages) looks blank to me...


As for visualizing molecules, IMV already has OR support, and looks good for animations, though I haven't tried it - http://www.molecular-visualization.com/

kryann
Level 2
Hi Guys,

Like you, I am quite interested in visualizing molecular structures in VR.

As it seems such software was missing, I decided to develop my own to assess the benefits of VR for this field.
It is called MolVR and you can download it for free here:

http://www.molvr.org/category/downloads/

I have also posted the application for review on oculus, but still haven't got any response.

At the moment, MolVR is still very basic, but you can load protein structures easily (Menu/Examples, or Menu/Load from DB). Note however that I have only included in my website 60 pdb structures that you can test (http://molvr.org/data/list).

The key 'c' allows to toggle Color Mapping (Atom / Residue / Chain / White).
You can also toggle automatic label display with the 'l' key and it display atoms label based on your distance to atoms.

The 'd' key toggles the Depth of Field effect. You can change focal distance using shift +/- and size of the focal region using shift left/right arrows.

You can keep track of the fps by pressing the 'f' key. Note that to achieve good VR, you should be at 75 fps. If your graphic card doesn't handle big molecules, you will probably be at 37.5 fps.. it still works but you can have some superposition of images during fast movements.

As soon as I can, I'll update MolVR to integrate other representations (only spheres/VdW as of now) and settings (rendering quality, etc). I am also working on rendering quality and speed.

Bests

DaftnDirect
Volunteer Moderator
Volunteer Moderator
I thought about this a while ago... after looking at Titans of Space.
I'd like to see DrashVR do something like this... sort of the opposite of Titans, scale-wise. Would be an amazing education experience.

Intel 5820K OC@4Ghz, Titan X (Maxwell), 32GB Corsair Vengeance DDR4, ASRock X99 Taichi, Samsung 500Gb 960 Evo M.2, Corsair H100i v2 Cooler, Inateck KTU3FR-4P USB 3 card, Windows 10 Pro v21H2 (19044.2075)

Anonymous
Not applicable

I was testing the MolVR 0.8 Win 64 build with Oculsu Rift CV1. It does not activate the HMD at all ...

Maybe you should update the Unreal plugin to a CV1 compatible ? Generally do you thing to make such code in Unreal engine have sense ? Plain OpenGL + manual adding of the VR support can make the specialized fine-toning required for real scientific work possible ....

Anonymous
Not applicable
One more thing - the graphic you use is relay nice, unfortunately it doe not work correct. The image (on 2D screen, Ocuslus Rift does not work) look a bit flashing with small oscillation. Looks like the pixel shaders get changing input.

Anonymous
Not applicable
The best code to show molecules on Rift is definitely UnityMol. I was testing latest version controled by hands through leap motion and it works perfect. I had developed several test codes myself, but I have no chance to compete with UnityMol.

gmaciocci
Level 4
I work for a large Open Access journal, and we're always looking to showcase the latest technology innovations to help accelerate discovery and the sharing of scientific research.

I'd be interested in talking to anyone with proven skills to develop a prototype for an embeddable, 2D and WebVR-compliant, open source molecular visualisation tool that could be used to enhance the display of a figure on an online manuscript with VR visualisation and basic interaction capabilities, while maintaining an interactive 2D fallback mode such as JSMol for people without headsets. 

If you're working on something like this, and would like a built-in audience to showcase your work (as well as direct collaboration with experts in the publishing field), feel free to PM me. 

bigmike20vt
Level 14


Has anyone gotten a biomolecular viewer working with the Oculus Rift yet? This was one of my primary motivations for getting this, and just wondering what work has already been done on this. Here are a couple of programs that this could be made to work with:



http://www.ks.uiuc.edu/Research/vmd/ (my favorite)



http://accelrys.com/resource-center/downloads/freeware/index.html



I can already view in 3D with VMD, by setting Stereo to side by side, but there is no distortion and I don't know how to get the headtracker to work.



CountBorgula


now i have visions of "Rasmol" in VR....  flashbacks of 1994 at university !.
Fiat Coupe, gone. 350Z gone. Dirty nappies, no sleep & practical transport incoming. Thank goodness for VR 🙂

Hiro_Protag0nist
Level 13

oasismark said:

Hi



Im very new to the whole OC scene, but i think it can of much use to my university.



We currently have a VR suite, its a huge projector screen with 3D projector and glasses, programs used is Virtalis VR for Pymol 1.2



I dont personally use it so forgive my lack of knowledge.



Is there any updates on Rift support for these or any other protein structures programs, last update to this thread was 6 months ago.



Id love to be able to replace a whole room and expensive projector with relatively inexpensive Oculus Rift



Thanks



Mark


I read that Virtalis have built-in support for the Rift in their premium CAD software and their entry level VR CAD viewer:

http://www.eurekamagazine.co.uk/design-engineering-news/virtalis-launches-worlds-first-affordable-vr...

Not sure if it would work for that Pymol application.


ottomanbob
Level 2
Check out Nanome. They do both drug design and math viz on oculus.