Question: Visualization of protein structure in R (Shiny)
1
gravatar for aquaq
5 weeks ago by
aquaq30
aquaq30 wrote:

Hi All!

I am creating a Shiny server and would like to show the user protein structures from PDB file. I tried to search for a package that is able to do that, but could not find one. bio3d can write the output to open by pymol and Rpdb have a visualization, but unfortunately it is not very good....

Is there any package or workaround that I am not aware of? Or any workaround if cannot be done by a package?

Thank you!

ADD COMMENTlink written 5 weeks ago by aquaq30
1

Don't know much about Shiny, but as its web based, can you make use of JSmol/Jmol or something?

ADD REPLYlink written 5 weeks ago by Joe18k

Thanks, I will look into it!

ADD REPLYlink written 4 weeks ago by aquaq30

PV is great for this, but it's JS not R

ADD REPLYlink written 5 weeks ago by JC11k

Actually if you make use of ShinyJS you can integrate any JavaScript library quite easily in your shiny application. I don't know how the 3D animation will integrate with shiny objects though, but it is worth a try

ADD REPLYlink written 4 weeks ago by pacome.pr50

Thank you both, I hoped to avoid messing around with JS, but these seem good.

ADD REPLYlink written 4 weeks ago by aquaq30

Are you hoping to display a dynamic structure or just a static one? If it's the latter, you could perhaps simply fetch an image of the protein from PDB and display that directly?

ADD REPLYlink written 4 weeks ago by Dunois150

Thank you for the answer. I have custom PDB files, I cannot just fetch unfortunately

ADD REPLYlink written 4 weeks ago by aquaq30
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