Easiest way to export svg/pdf/png?

[bananabenana]

Hi,

Really love this tool and have made some awesome html-based figures. Do you have any guidance on the best way to export highres svg/pdf/png figures from this? Or natively from the r3dmol object?

# Load pdb file
pdb <- bio3d::read.pdb("I7AVL3.pdb")

# Generate r3dmol
ribbon_structure <- r3dmol() %>% 
  m_add_models(m_bio3d(pdb)) %>% 
  m_set_style(m_style_cartoon(color = "white")) %>% 
  m_set_background_color(gray(0.9)) %>% 
  m_add_outline()

# Save as html
htmltools::save_html(ribbon_structure, file = "ribbon_structure.html")

Thanks

[swsoyee]

Hi, you could use function m_png to export a png figure
https://swsoyee.github.io/r3dmol/reference/m_png.html

[bananabenana]

Hi, thanks for your fast response. Apologies for not getting this yet.

So if I run the following:

ribbon_structure_png <- r3dmol() %>% 
  m_add_models(m_bio3d(pdb)) %>% 
  m_set_style(m_style_cartoon(color = "white")) %>% 
  m_set_background_color(gray(0.9)) %>% 
  m_add_outline()
  m_png()

How do I then save this object as a .png to disk and control resolution etc? I am using RStudio.

[swsoyee]

Sorry, it didn't support resolution and save to disk options.

r3dmol/inst/htmlwidgets/r3dmol.js

Lines 200 to 209 in 0eefc1c

	pngURI: (params) => {
	viewer.render();
	const width = params.width || viewer.getCanvas().getAttribute('width') / 2;
	const height = params.height || viewer.getCanvas().getAttribute('height') / 2;
	const captureDelay = promiseCalls.length === 0 ? 0 : params.captureDelay;
	window.setTimeout(
	() => { container.innerHTML = `<img src="${viewer.pngURI()}" width="${width}" height="${height}"/>`; },
	captureDelay,
	);
	},

You could set the size of viewer (https://swsoyee.github.io/r3dmol/reference/init.html), right click and save the image directly.

[bananabenana]

Okay great, thanks for your help! Also once again, amazing software which we are using in an upcoming paper!