I love pictures. And photographs. Unlike some, I can’t paint or draw with any great skill, but in common with many other people I get immense pleasure from photography. I’m no expert and wouldn’t even consider myself a serious hobbyist, but I have been known to enjoy composing and capturing an image with my little compact camera.
Here’s one I took the weekend before last when we were at Brighton. I now have it as the desktop picture on my computer and it has been making me smile ever since. I like the elemental quality of the scene: earth, water and sky and my children caught in a moment of simple enjoyment.
Pictures are also important in my work. But the pleasure of their creation is sometimes mixed with pain. Lots of pain.
In the past few days I have been working on a new paper which will describe the structure of a protein-peptide complex that we have solved in my lab. It’s been tough enough grinding out the words to describe our results, but coming up with the figures has been about a thousand times harder. Hence the well known epigram, I suppose.
Although I have images of the structure in my mind when I’m writing, I have to lay out the paper in words first to find out what it is I want to say, to identify those parts of the structure that are likely to be the most meaningful for the reader. Once the draft manuscript is complete I can list the figures I’d like to include.
But this is when the trouble starts.
Often the list is quite long and has more images than can be accommodated in the finished manuscript. (Colour figures are not cheap, so cost is a major consideration.) But how to condense all that information, without obscuring the message? The meaning of a good figure should leap off the page; ideally the reader shouldn’t even have to consult the legend to appreciate the central message. For structural biologists the principal difficulty is trying to convey detailed three-dimensional information on a two-dimensional page. It requires real artistry, and perhaps that is the solution?
In the early part of the 20th century Picasso and Braque pioneered cubism, a school of painting that tried to be a way of depicting an object as seen from different viewpoints independently. In other words, the artist depicts the subject from a multitude of viewpoints to represent the subject in a greater context. Here’s an example:
In the words of the celebrated Australian artist, Rolf Harris, “Can you tell what is it yet?” Fortunately this image does come with a figure legend. It reads, “Le guitariste.”
But of course!
I don’t mean to mock: Picasso was clearly a very considerable artist (though I don’t go for everything that he produced). But clearly the aim of the cubist is different to that of the crystallographer*. We work on very different planes of understanding. The idea of being able to present different perspectives in a single image is appealing, though in my work as a scientist I’m looking for literal—rather than conceptual—representations of reality. I guess my problems are a bit more prosaic, but I do still struggle for my art.
Let me show you what I mean. Here’s an image showing the superposition of the protein structure before (grey) and after (purple) binding of the peptide (orange):
_All structural figures made with Warren Delano’s fantastic PyMOL
The image is schematic since, rather than depicting all the atoms of the molecule, you see a winding worm tracing the fold of the polypeptide backbone. But I’ve also shown (in sticks) some of the side-chains of the protein that change their conformations when the peptide binds. The aim here was to show global and local conformational changes that resulted from peptide binding.
The second figure below was an effort to show some of the bonding pattern that locks the peptide and protein together:
The green dashed lines show hydrogen bonds formed between the backbones of the peptide and the protein. There are nine of them in total and they help to zip the peptide into place. The trick here was to find a viewpoint that allowed all nine to be seen. Also, I didn’t want to deviate too much from the viewpoint of the previous figure. I didn’t want to lose the viewer.
But I wasn’t happy with these images – something gnawed at me overnight. It struck me that the two views weren’t so dissimilar; perhaps they could be combined into a single figure? I thought about how to do that and came up with this:
Here instead of wormy tracery I have depicted the bonds connecting the backbone atoms as sticks. But the zig-zag path of the backbone is untidy – it clutters the view and obscures our perception of the side-chains. This wasn’t the answer.
So finally I thought to simplify still further. I opted to return to the smooth backbone trace, even though it doesn’t show all the atoms involved in hydrogen bonding to the peptide backbone, because, this doesn’t really matter. The key point is to show that the bonds are distributed along almost the entire length of the peptide (and most readers will already know that proteins are capable of these interactions).
Sharp-eyed readers may have noticed that I also zoomed in a little – to capture as much detail as possible while still showing enough of the overall structure to preserve the context of the peptide binding site. This is better but I’m still not wholly satisfied with the result. I’m not sure about sticking with the green hydrogen bonds; maybe I should switch to purple or lilac, so that it is clear that the peptide is bound to the purple, rather than to the grey structure?
This tortuous process occurred over a period of three days. And these weren’t the only figures that I have been wrestling with. Each image demanded a similar level of attention, scrutiny, effort and engendered immense frustration. And in every case there was the wretched struggle to twist and turn the viewpoint so that all the important features remain in view. Like Picasso and Braque, what I really needed was to find a way to show different perspectives in the same image. And I think I’ve found an answer, though it can’t yet be implemented on paper, alas.
What I really need are moving pictures.
*Curiously, Picasso was acquainted with at least one crystallographer, JD Bernal, a Professor at Birkbeck College in London. During a party at Bernal’s flat in Torrington Square in 1950 Picasso famously sketched a pair of angels on the wall. The plaster containing the drawing was saved when the building was demolished and later bought by the Wellcome Trust. For £250,000.
[takes note of the footnote]
[takes note of Eva’s comment]. But is a bit nonplussed.
The movie’s helpful, maybe an eye-poppin’ stereo. I’m super-intrigued by the Bernal mural- was it inspired by discussions of crystallography?
I can understand your frustration. Do you get to put movies in your supplimental data?
Perhaps as time goes on (and I have nothing but intuition telling me this doesn’t happen now) people will read more online where they’ll have access to embedded vidoe content. Maybe we’ll all be using Kindle(tm) readers for our literature reading on the train/bus…
Oh grief Stephen. Been there, done that, as well you know. Well written.
I thought that picture of your family was me for a minute:
When the movie adds to the information imparted, I always click on the link. And in “live” biology, the photos can be sooooo important, too. My lab members are always on at me about how picky I am, starting from the snapshot, and continuing with Photoshop. I mean contrast, light and hue adjustment for that, generally. Dust outside the tissue section, centering the cells in a culture shot – anything that is distracting and for which one automatically filters when looking at the real thing. And usually, there are multiple small parts for a given figure, so there are major considerations of page layout, getting margins to line up and letter sizing clear and right. Sigh. (Thinking of all the figures that need to be done.)
@Sarbjit – I tend not to use stereo-pairs in papers these days since most people can’t see them easily (they lack the facility or the viewer). It’s generally better to try to cater for the majority mono audience, even if that entails a lot of tweaking (and frustration).
The mural can be seen here – it doesn’t stand out very well but the picture is of a man and a woman, wreathed and with wings. Not sure of the significance, though I believe it was done at Bernal’s request. History does not record whether Bernal made a reciprocal visit and sketched a space-group diagram on Picasso’s wall…
(From the Daily Telegraph)
@Ian – Yes, you can usually submit movies as Supp Info, though they’re not always to hand when you want them. And some of the movies that people make aren’t that helpful – a rapid 360° rotation is often what you get.
However, you’re right that technology will probably provide the answer, thought the Kindle will need to develop a colour screen to be really useful for presenting structural biology or other 3D information. There was an interesting development in pdf technology recently which allows protein structures to be embedded at 3D object within a pdf file – see this paper in TIBS for an example.
@Richard – ta. Interesting photographic comparison: southern hemisphere – hats; northern hemisphere – no hats.
@Heather – I see the pain is widespread. I trust you only use Photoshop after the microscopy and not before! 😉
But yes, video is tremendously powerful when used well – no amount of stills can match it. I find it especially revealing when calculating ‘morphs’ which show a smooth transition from one structural state to another. I’ve done one for this present paper but maybe that’ll be the subject of another post…
Interesting photographic comparison: southern hemisphere – hats; northern hemisphere – no hats
We have hats in the Northern Hemisphere, too, except that we lose them.
Your quest for simplicity suggests that what you need isn’t a video, but a schematic, showing the interactions at the expense of the actual shape of the structure. Kinda like the map of the London Underground emphasizes connections over geographic distance (while maintaining topological relations), because that’s what tube travelers want to know.
Sorry to hear about your hat – hope you might get it back somehow.
I was aiming more for clarity than simplicity — as well as being able to show several things in the same figure (_e.g._ main-chain and side-chain movements on peptide binding as well as the hydrogen-bonding pattern). A schematic would work for the H-bonds but not for the other demands of the figure.
As much as I like the last version of your diagram, Stephen, it doesn’t capture the 3D shape of the peptide as well as does the the movie. We have a similar problem in teaching embryology, where there are 3D structures that change shape (with the added problem of growth), often in a fairly complex manner. There are some animations available online, but they’re not always accurate or instructive. I can make and manipulate polymer clay models for small group instruction, but that’s of no use for the large groups (200+) to which I teach embryology.
Some would argue that medical students don’t really need to know anything about basic morphogenesis, but a) it’s very frustrating for many students, to receive only handwaving from the instructor on complex topics, and b) a basic knowledge of some morphogenetic events (neurulation, gut rotation, palate formation, partitioning of the bulbis cordis and truncus arteriosus) is required to understand various developmental anomalies. Perhaps I’ll eventually find the money and time to make a series of embryology podcasts/videos, using the polymer clay models.
And thanks for linking my post. 😉
You’re absolutely right Kristi, video is the way to go for 3D info but I guess we’re some years away from having the technology to implement it it in an accessible/ portable format. The means of production are getting much cheaper and easier though so I hope you will find a way to get recording.
You’re welcome for the link – I _loved_your rattlesnake picture – fabulous!
bulbis cordis > bulbus cordis
I’ll need a proofreader as well … heh.
OT, but does NN have a representative at the Lindau Nobel Laureate meeting?
I need a proof-reader too: can’t even do italics, never mind spelling. Bulbis (sic) cordis I didn’t notice.
Clickable and pop-up and 3D PDFs will be really useful for exactly this type of publication, but in the future I think.
Fascinating. I did think the first attempt was pretty clear to be honest, but that video made it really stand out. What a difference! Seems to me to be an ideal contender for those 3D diagrams which require a pair of green and red glasses. Bit low tech, though, I guess. And the journal would have to provide the glasses, I guess.
@Clare – I’m afraid the red/green mode of stereo wouldn’t be much cop since that drains all the colour from the figure.
People do use ‘stereo pairs’ which allow 3D viewing on the page but there is a knack to it. Try this:
You have to put your head reasonably close to the screen and allow your eyes to defocus a little. You should start to see the two images merge in the middle – try to focus on the merged image (or relax your eyes to bring equivalent parts of the structure together). Try to ignore the residual images that you can see on either side. It took me quite a while to be able to do this, though others pick it up easily; I can only do it if I take my specs off (I’m short-sighted).
Who can manage it? Any other tips on how to make it work?
Cough.
That’s odd. Did my comment disappear?
I was point at this widget anyway.
And now it’s back. Did I get spam-trapped?
Yes, Richard, you did. Comments consisting of just a single link tend to get automatically flagged as spam.
That’ll learn ya. Anyway – thanks for the link, Richard. Funny how language changes though: when I read ‘widget’ I assumed you would be directing me to some sort of software tool, not a thing made from atoms.
Anyway, as discussed on your thread, the viewers are a bit pricey. It’s more fun to try to see the stereo-figures unaided. Though it will hurt your eyes after about 6 hours of trying…
Ah, but on that thread there’s also a hint how they can be less pricey.
And it’s only fun until someone loses an eye.
Watching 3D structures always takes me back to seeing rabbits in swirly patterns in those Magid Eye books. Always so disappointing now, though: “Oh. It’s a protein structure, again. I really thought this one would be a dolphin.”
Funny you should say that Eva, because sometimes I look at a protein structure and all I can see is a rabbit!
_A rabbit or seryl tRNA synthetase
Ugh, I can’t do that. Probably my useless eye sight – I can never do those magic eye pictures Eva mentions either. Not ever, once. It’s really irritating. I can see the rabbit though. 🙂
Just gone to Richard’s link and found he can’t either. The only person I’ve ever met who can’t! I wonder why not. Is it dominance/lack of dominance of one eye…or something…
Perhaps I’m just used to seeing what’s really there?
Don’t be hard on yourself Clare – it is very tricky to do and took me a long time ‘get it’. Have you ever tried that trick of putting your outstretched index fingers together in front of your face and relaxing your eyes so that you can see a ‘finger sausage’ (for want of a better phrase) hovering before you? If you can manage that, have another go with the stereo-pair.
@Richard – Perhaps I’m just used to seeing what’s really there?
Yes, but your brain tricks you into seeing 3D all day long from two 2D images..
@Clare For some long-forgotten historic reason I have 100 pairs (or so) of the goggles Richard was talking about in my filing cabinet. I only really need 99 or so pairs, so can spare one!
I don’t seem to be able to do the stereo-pair thing without the viewer – I can make the two halves go all squirly, but never get them to line up correctly. Probably because I’m wearing glasses or something (without them on, maybe I could do it, but it would be all fuzzy, so what would be the point?).
I enjoyed this post, Stephen – a nice little view into the headaches of making the figure look “just so”. I tend to spend way too much time doing this with (non-scientific) photographs and Photoshop, so can sympathize with the effort required, in a way.
And I enjoyed the Brighton beach photo – been a very, very long time since I was there (late 70’s, probably – maybe even earlier).
I can’t do it with specs on either but have the advantage of being short-sighted.
I see what you mean about the work that you put into your photos:
_From Richard’s page on Flickr
Nice.
Ooo, thanks for the shout out, Stephen. 🙂
It’s not a multi-colour actin stain, by the way… 🙁