You know those stereo images so belovéd of structural-type people? The ones you get in journals where you’re supposed to be able to squint somehow and see it in 3-D?
I’ve never been able to pull off that trick. Never been able to see those silly ‘Magic Eye’ things either. Must be something to do with being a predator — evolutionarily it’s good to see what’s really there, rather than some abstract shape that may or may not be lunch, or in the worst case, something with sharper teeth and bigger claws than me.
Which, if structural biology is in the genes, probably puts my children at an evolutionary disadvantage, but hey.
Three-dimensional visualization of protein structures is not to be dismissed lightly. You cannot truly grok a protein structure until you have seen it in 3-D, run your fingers lightly over its crevasses and curves, felt its binding pockets and smelled its van der Waals radii.
(Maybe that latter was a bit too poetic).
I tend to do all that on a screen, with 3-D glasses. The first time a lysine side-chain brushes your nose you’ll never want to go back to 2-D. But it’s (a) quite expensive to get 3-D on LCD screens and (b) everyone prints the figures out anyway. So structural biologists are wont to print stereo diagrams in their papers. My previous boss, who must have suffered from the same sort of evolutionary history, kept a set of viewers in his drawer. These are two glass lenses in a metal frame, with swinging metal legs so that you could place the things over a picture, peer down and see in stereo. Very useful, simple to operate, and almost impossible to replace if stolen lost or broken.
So for the last couple of years I’ve been reduced to either squinting (and looking out for larger predators) or giving up in disgust, going to the PDB, downloading the files and trying to imagine it in 3-D by rotating the thing on my screen.
But a couple of weeks ago in the office I came across a veritable wonder of modern technology. Ladles and gentlespoons, I present the Stereopticon 707:
This flimsy bit of card with two plastic lenses actually folds flat, and what’s more, does exactly what it claims to. It is so simple, so easy to use and cheap that I can’t help thinking it should come with every undergraduate textbook.
Side elevation
Isn’t she just wonderful?
Someone in Jennifer’s lab has probably already improvised one of these out of three used eppies, a petri dish and five Weetabix box tops.
Five? Tosh. Only need four.
Richard, that’s a beautiful post. I wasn’t able to see those Magic Eye pictures either, until someone taught me a special secret. If you’re very nice, I might impart it. Wouldn’t want you to get eaten by a tiger.
I sympathise – this used to defeat me, as did those funky Magic Eye posters, though infuriatingly my wife could get them to snap into view with ease (a skill developed from long hours at school staring vacantly into space, she told me).
However, don’t lose heart because it is possible to train yourself to do it. As a crystallographer myself, I felt somehow incomplete without this facility and spent some hours focusing and defocusing my eyes. Eventually I cracked it; in my case, since I’m short-sighted, I found I can only do it with my glasses off. Am now working on my other crystallographic deficiencies…
In which vein, given your recent artwork, can you give me three good reasons to switch from O to Coot…
I have one of these. It came with a chemistry textbook, and at the time I didn’t even know that I could have just my Magic Eye picture finding skills to see stereo structures without the viewer.
And Stephen is right, you can train yourself. (I learned by pretending the paper was transparent and I was looking through it to an object behind it.)
I can do stereo pairs but have never managed magic eye pics either. I go through life realising that I am severely missing out on exciting secrets that the rest of the world knows but I don’t (and nor does Richard, I now learn).
I’d very much like one of those Stereopticon folding X-ray specs thingies. It’s not just structural biologists who use stereo pictures – palaeontologists do, too, so they can get some idea of the structure of a complicated bony widget that just can’t be imagined very easily from a 2D picture. And I, too, can’t get them to bounce into 3D
lifedeath just by staring at them, and neither do I have any luck with magic-eye pictures. The problem does remind me of a Two Ronnies news item that went something like this: and we’ve just heard that the great tiger-hunter Digby “Shoot-‘Em-Between-The-Eyes” Fortescue has just been killed by two one-eyed tigers working closely together.Spy Kids 3D, anyone?
Chemists use stereo pictures too for molecular structures (not proteins, but ball-and-stick smaller molecules)
@Henry: I’d very much like one of those Stereopticon folding X-ray specs thingies
You can get them from the link that Richard gave, or from Hampton Research. A bit pricey but perhaps you can persuade the editorial office that a pack of 10 is required?
All this talk of 3D reminded me of the ViewMaster toy I had as a child. I remember having a disc with pictures of Bugs Bunny and, although I was aware that the pictures somehow looked different, it wasn’t till later that I realised it was a 3D effect! Bit slow on the uptake. Later – much later – I experimented with 3D photography but there’s something rather eerie about 3D stills and I gave it up. Happily I can still share Richard’s excitement at being able to peer into the nooks and crannies of a new protein structure, though I confess I still don’t know what a Van der Waals radius smells like…
I still don’t know what a Van der Waals radius smells like. French mustard with a hint of cinnamon, and a finish redolent of summer fruits and burning truck tyres.
…finish redolent of summer fruits and burning truck tyres.
No, no Henry, those are Van der Waal radials.
ba-boom tish.
My goodness. Hampton are charging ten quid per? For a bit of printed card and lenses that are $1.30 a pair? That markup is nearly as good as that on miniprep kits (rant at the other place brewing).
perhaps you should host a ‘Tips and Techniques’ session at the NN conference? Looks like you’d get at least three attendees. Maybe it should be (yet another?) panel, and I could share the secret of my superpower, too.
@Stephen – but can you do it in the twenty seconds some speaker leaves it up on the screen during a talk? Putting stereoscopic image*s* in a talk always annoys me – especially nowadays when it’s possible to integrate a little animated film to show them to best advantage. Or just show one eye’s worth.
@Heather – no I can’t do it from that distance; I need to be bent over the page. I agree it is silly of speakers to try to use stereo-pairs in talks, though with the right set-up (two projectors, metallic screen and polarised glasses) I have seen it work well (once!). You’re right that these days it is much better to use an appropriate animation in a talk – my preferred method is a slowly oscillating rendition (~15°) of the portion of interest.
Even in papers I tend to avoid using stereo-figures, assuming that most people can’t see them (and don’t have a Stereopticon707 to hand either). I think it’s better to spend time making an accessible single image, though it can sometimes be exasperating trying to find a viewpoint where everything you want to show is visible!
Structure papers can’t have too many (mono) figures, Stephen!
Well, within budgetary constraints of course: charges for colour figures are still fairly outrageous in some journals. But actually I was referring more to the problem – that I have often encountered – of trying to find an orientation of, say, a ligand binding site in which residue X isn’t hidden behind residue Y and doesn’t have a side-on view of that pesky tryptophan so that you can immediately see it’s an aromatic group. I’m sure you know what I mean!
Exactly what you mean, Stephen. I think I spend more time getting figures just so – for talks and papers – than the actual writing.
Proteins are three dimensional?
I thought they looked like this _ on a good Western, and like this ~ on a bad one.
No wonder they took away your Gilson, Cath.
😉
(That was a really bad Western).
I voluntarily laid down my Gilson 3 years ago and haven’t missed it much since…
_ I think I spend more time getting figures just so – for talks and papers – than the actual writing._
Agreed. I was going to add a crack like “And do the plebs appreciate the effort?” but decided to hold my (f)ire. And then along comes Cath! That woman needs a renaissance…
Do they appreciate the effort?
Any non-structural people here who read structural information-containing papers?
Nope, sorry – I just can’t ever “see” 3-D structures in the way the presenter seems to intend. I can’t make my brain process the images in the right way or something.
Have you been eaten by a tiger recently?
Me. Rarely. But I like the pretty PDB pictures, especially when they link into the genome browser at UCSC. But I probably need more arrows to show me what to look at than you do when you come across a histological section.
When I’ve got a little more time (you can tell I’m really busy right now, right?) I’ll talk a little more about my best structure ever, and show how lovely it is – 3D is really necessary for full effect (and when we first saw it, we didn’t realize it ourselves), but I’ll try to use a movie for that.
Have you been eaten by a tiger recently?
Who, me?
Yes, you.
No, but I have been distracted by the recent and mysterious appearance of a big hot yellow thing in the sky; a sky that has turned a very strange colour that is not grey. The residents of this fine city are consulting oracles, slaughtering goats, and praying to the hockey gods in our confusion.
thinks
Canadian seasons are snow, ice, slush and construction, yes? The big yellow thing is probably an orbiting JCB, preparing to make a bypass.
Starting in January, I measure the year by the following seasons:
Skiing
Whining about the weather
Kayaking
Whining about the weather
There is a bimodal peak in my blogging output. Guess which seasons?
I haven’t heard any really bad poetry coming from on high, so I would have to doubt the JCB hypothesis.
Odd timing stuff, there. I assure you I didn’t take 13 minutes to write the last comment. Nor have I inspected the inside of a tiger’s pharynx recently.
We seem to have recovered many of Vancouver’s clouds here. You wouldn’t want to be kayaking the Garonne right now unless you like your water extremely brown and turbulent.
People in my lab have started playing with the ImageJ plug-in that lets you make 3-D rotating models of your slices. I thought it was gimmicky until I sat down and seriously watched a few of these videos. It’s amazing what you think your brain can fill in from a series of 2-D sections, compared to its actual miserable failure to do it properly when confronted with a proper job of it.
Or maybe that’s just my brain.
Just come here from the future. I’d love to see this in front of me. Looks really good….
My brain just imploded.