3Dmol.js with {r3dmol}

[Former user]

Hi all!

Just thought I would share a package I've been working on for visualisation of pdbs (and bio3d objects) inside Rstudio / Rmarkdown documents.

{r3dmol} website

It utilises the 3Dmol.js framework to create the 3D interactive viewer.

I'm working on supporting various {bio3d} analysis outputs, to colour based on RMSF / add lines based on dccm analysis etc. Any feedback and ideas would be appreciated!

[Brady]

I realised that I posted this while not signed - but this was from me! Keep up the great work with {bio3d} as well, I use this package constantly!

[Xinqiu Yao]

Hi Brady,

Thanks for the suggestion! It looks very interesting. Indeed, 3D visualization would be a powerful component of bio3d. We actually have a package called bio3d.view in development. It would be interesting to compare and see how they may work collaboratively.

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[Brady]

I did try to dig in but couldn’t find any details regarding bio3d.view - so I assumed the development may have paused or was going on internally. Would love to test it out though and see how it all worked, and as you said, compare and potentially collaborate between the two.

[Lars Skjærven]

Nice! It looks fantastic. Would be interesting to see how it could be developed to match up with other output of bio3d, perhaps in particular pdbs objects (aligned ensemble of pdb structures), PCA, NMA, and perhaps eDDM (https://bitbucket.org/Grantlab/bio3d-eddm/src/master/).

I’ll try it out in more detail.

The mentioned bio3d.view project (https://bitbucket.org/Grantlab/bio3d-view/src/master/) has been idling for some time now, but ee do use in our bio3d-web project (https://bitbucket.org/Grantlab/bio3d-web/src/master/) for simplified representations of protein ensembles in browser. I guess r3dmol could potentially take over that job ?

[Brady]

The viewer has full support for Shiny functionality so it should be able to work inside the bio3d-web project without too much trouble.

Certainly we would like to add more support for the other outputs of bio3d. Currently you can add multiple models with m_add_models() if you first convert the pdbs object to a multiple-structure pdb first. It can also handle trajectory files with m_add_models_as_frames().

Please do get in contact over at the github for it: https://github.com/swsoyee/r3dmol or just me contacting me here. Would love to focus on developing particular features for the package that can be useful with bio3d.