Jolecule

January 26, 2011 8:03 AM

Jolecule is an HTML5 viewer for three-dimensional protein structures that requires no plugins. "Jolecule works in modern browsers such as Chrome and Safari and mostly in Firefox." Check out the 3D structure of myoglobin. Or view an animated slideshow of how the glucocorticoid receptor binds DNA (press spacebar to advance).
posted by grouse (21 comments total)

Via Reddit.
posted by grouse at 8:04 AM on January 26, 2011

Neat. It's based on canvas, with a simple vector library and about 17k of rendering code. In theory you would choose WebGL to do a 3d view like this, but my guess is it wouldn't work very reliably.

The author is Bosco Ho.
posted by Nelson at 8:13 AM on January 26, 2011 [2 favorites]

That's interesting. I wish I knew more about chemistry.
posted by delmoi at 8:15 AM on January 26, 2011

how cool! I just emailed this link to my hubby, who does org chem protein synthesis :)
posted by supermedusa at 8:38 AM on January 26, 2011

"This Google App Engine application is temporarily over its serving quota. Please try again later."

This cloud, it is like Geocities, no?
posted by eeeeeez at 9:09 AM on January 26, 2011 [13 favorites]

Awww, fuck.
posted by grouse at 9:21 AM on January 26, 2011 [1 favorite]

Arrrrgh. Over quota indeed.

I'm one of those people who seems to think in pictures and then applies the words and has trouble taking a purely text description of a complex structure or relationships and deriving a picture from them (can do in 3-D, gets harder with more dimensions).

This sounds like an excellent 'shared whiteboard' tool for figuring out how things fit together.

(If anyone understands the components and connections of multiple virtual machines based on a single original virtual machine under VirtualBox 4, for example, I'm a naive new user looking for a picture ....).

Harrumph. Hey, Google, you can use some of the gazillion unused bytes you claim to have reserved and waiting for me in gmail, any time.
posted by hank at 9:47 AM on January 26, 2011

(hank, the bytes you have in GMail are storage, not bandwidth; it's the difference between the size of a water tank and the diameter of the hose emptying it. I guess the internet is a series of tubes.)
posted by Fraxas at 9:50 AM on January 26, 2011 [1 favorite]

This sounded cool. Which of the Google App Engine quotas did they exceed, I wonder?
posted by artlung at 9:57 AM on January 26, 2011

It would be excellent to have a standard browser-only, no-plugin-required viewer for complex chmical structures. Current best practices are i) jpegs, ii) jmol (java applet) or iii) the chemdraw plugin which has always been a problematic piece of software. There's a real problem here to be solved.

Does anyone know what spec it's using for structure data, SMILES or PDB, for example? I wonder if it can handle .mols/xyz or cifs.
posted by bonehead at 10:02 AM on January 26, 2011 [3 favorites]

Based on this comment, I think they are using pdb.
posted by artlung at 11:04 AM on January 26, 2011

Bummer. I wanted to check this out. Damn the cloud.
posted by thsmchnekllsfascists at 1:38 PM on January 26, 2011

Jolecule is back up now.
posted by grouse at 4:50 PM on January 26, 2011

Clicking and dragging rotates the model freely. You can use the shift key to zoom and rotate about the z-axis.
posted by Blazecock Pileon at 5:26 PM on January 26, 2011

Sick of complicated protein viewers?
That is uncanny. I was just sitting here thinking how sick I am of complicated protein viewers and then... presto!
posted by jcworth at 7:53 PM on January 26, 2011

Neat! Being able to highlight specific residues instead of having to hunt them down by mousing over the 3D structure is a definite plus.

Too bad the graphics aren't quite as shiney as jmol (and lacks ribbon types), and "show ligand" doesn't seem to work for the receptor I was looking at (worked fine in jmol). It was a little chunky spinning around even on an i7 with the latest Firefox (it could be FF's fault, but jmol is super-duper responsive).

Again, neat, but it's not something that I could/would use over jmol. Yet. Hopefully.

Yeah, damn, I really like the highlight residue list. I really really like that damned feature.
posted by porpoise at 8:17 PM on January 26, 2011

(it could be FF's fault, but jmol is super-duper responsive).

Idk about jmol, but this is almost definitely ff's fault on an i7. FF has notoriously dismal JS performance.
posted by thsmchnekllsfascists at 6:51 AM on January 27, 2011

Jolecule (html5) was really unresponsive, jmol (powered by JS) is silky smooth.
posted by porpoise at 7:28 AM on January 27, 2011

I just checked it out. jmol is a java applet.

Jolecule uses browser-native JS rendering via the <canvas> tag. Firefox 3 has terrible JS performance. That's why it sucks in FF 3. FF 4 is supposed to be much more responsive though.
posted by thsmchnekllsfascists at 7:46 AM on January 27, 2011

Jmol is a great peice of software, but it's in java, which brings in that whole host of problems. We've got it disabled on a bunch of higher-security machines at work, and java starting tends to bring these old computers to their needs for a few minutes as it starts. Jmols is fabulous, but java isn't.
posted by bonehead at 9:28 AM on January 27, 2011

s/needs/knees/

Damn autocorrect.
posted by bonehead at 9:49 AM on January 27, 2011