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My PyMol models and figures | Molecular Art

My PyMol models and figures

Figures from a recent publication – The Dinosaurs of the  complement system

The below figure is created from two manual build PDB models: the large membrane floor and the “dinosaurs” or rather the MBL oligomer of the lectin pathway. Instead of using the standard PyMol surface representation i opted to use the Isosurface function which i find easier to customize to my likings and obtaining the look I wanted. The cell membrane is based on an small atomic model of the core LPS layer from Pseudomonas Aeruginosa, which is duplicated a bunch of times before translating the copies in the X and Y directions, creating a seemingly single combined membrane.

MBL_park_membrane
The MBL molecules are placed on top of a homemade membrane depicting how trans activation could occur on the surface of an activator.

The MBL models with their extended MASP molecules somewhat resembles some of the giant dinosaurs which is why I call the figure “The dinosaures of the complement system“.

The below figure is basically a top-down view of a combined model of two of the MBL molecules from the top figure, showing how they may interact with each other. The membrane is the same as in the top figure, only smaller.

7mer_top_mem8

The below figure is a recreation of a figure published by another researcher. The emphasis was meant to be on the two MASP molecules which are bend into the cone defined by the legs of MBL molecule, therefore they were given vibrant colors compared to the faint gray color of the MBL molecule.

figure

 Figures from my PhD thesis

While writing my PhD thesis I produced a ton of different figures, many of which was never used, because I was constantly pushing the boundaries for the quality and style I wanted in my thesis. I also had a very specific aim with my figures, as I wanted all of the models within a figure, to be to scale relative to each other. I was sick and tired of seeing high as well as low impact scientific papers, getting the scale completely wrong. Many reviews would e.g. completely misrepresent the scale of interacting proteins in their introductory overview figures either due to space issues or because they never bothered to look up the actual size of the proteins in question. So one misrepresentation could propagate down the following generation of  papers because no one bothered to check or think about it etc.

Thus I was highly motivated to not commit the same mistake in my thesis, although the number of ppl who would actually read my thesis could probably be tallied on two hands. I created atomic models of all the known proteins in the human complement system, carefully mirroring the actual size and domain architecture (if known) of each. For many models, where no crystal structure was known, I was forced to create composite domain models using similar and sizable domains from known unrelated structures and combine them based on published characterizations and structural studies.  Sometimes I simply just had to guess a bit,  as was the case with my favourite of the models, the C4 binding protein:

c4bp_6
My take on how the C4b binding protein may look like, inspired from various publications. BUT it is inherently wrong as I applied some artistic freedom with this one.

When it came to combining the single models within a figure, I was very alert as to not introduce any deliberate scale bias at this point in the process.

complement_components_lectin_v2 (RUKI home's conflicted copy 2012-11-23)
The lectin activation pathway of the complement system

Unfortunately I had to compromise slightly with the scale in the classical pathway figure concerning the antibodies, due to time constraints. I discovered the mistake at the day of my  PhD defence.

complement_components_classical_v4
The classical activation pathway of the complement system

complement_components_c4_degradation_v3 (RUKI home's conflicted copy 2012-11-23)

Factor I mediated degradation pathway of C4.
complement_terminal_test_3
The terminal pathway – sequential assembly of the membrane attack complex (MAC)

As is I am sure is evident from the above figures, I was (and still very much am) quite inspired by David Goodsells “Molecule of the Month” look. The Goodsell look can be obtained quite easily using the program QuteMol (however you cant do anything else with the program) or by using the Goodsell-like PyMol script from the PymolWiki gallery page. I used the latter option,  although in a slightly modified version. IMO the Goodsell look is at its best when you move a bit closer than in the above figures. Below I compare the domain and super-domain architecture of some of the related complement proteins using the Goodsell look.

c3_4_5_3b (RUKI home's conflicted copy 2012-11-23)
Surface representation of the crystal structures of human C3(PDB ID:2A73), C4 (PDB ID:4FXG), C5(PDB ID:3CU7) and C3b (PDB ID:2I07). The common multi-domain architecture is illustrated for the C4 crystal structure in panel A and B, which are related by a 180° degree rotation around the y-axis. The common super domain architecture is illustrated for: C4 (C), C3 (D), C5 (E) and C3b (F).

In every proteins crystallographic PhD thesis it is mandatory to show some electron density, and I of course also made quite a few electron density figures. I guess what sets my figures apart from the more classical electron density figures you see, is primarily that I took the time to use the map double setting in PyMol twice per rendering. This setting resamples your map at twice the resolution each time it is used, and you can use it as many times you want! Unfortunately it comes at an eightfold increase in memory use each time it is used, which logically slows down the process quite significantly and naturally the upper limit for the number of times it can be used is reached quite fast. However I think the end result is worth the extra processing time.

domain_den_c4 densityI also did a lot of electrostatic surface representations to visualize the electrostatic interaction properties of different interacting domains and proteins. This was done using the brilliant APBS plugin for PyMol as opposed to using the “generate vacuum electrostatic” function, which basically only performs a charge smoothing. APBS takes a bit of tinkering to use efficiently, but it is definitely worth it.

CCP_and_SP_exosite

 

I only did a couple of schematic figures for my thesis but I actually enjoyed making them as simple as possible while still containing the information I wanted to convey . The next two figures were made in something as simple as powerpoint. They is nothing fancy about them, just simplicity. They are also the two biggest errors in my thesis concerning my figures. I had from the start planed to color code the schematic figures with the structural figures, but for some reason it completely slipped my mind. Instead I color coded them to show which gene each chain originates from, which only makes sense in the MASP figure. But no one noticed so fuck it.

MASP-domains
Color coded to show which gene each chain originate from (blue+green= MASP-1, blue+brown=MASP-3, pink+yellow=MASP-2). Schematic representation of the domain architecture of MASP-1, MASP-2, MASP-3, and alternative splice products MAp19 and MAp44 depicting the intermolecular relationship of the domains. The disulfide bridges are only guiding, and do not represent the complete disulfide binding pattern.
domains_photo
Schematic representation of the chain architecture of C3, C4 and C5 depicturing the domain arrangement within each chain. The pictured disulfide bridges are only guiding, and do not represent the complete disulfide binding pattern.

The below figure took forever to make because I first had to learn how to use a new (for me that is) program called ChemSketch. The program is pretty good at drawing chemical structures in a  very fast and correct way. However it has a bit weird learning curve, but I got there. I used it for showing the catalytic mechanism of a serine proteinase.

catalytic_mechanism (RUKI home's conflicted copy 2012-11-23)
The catalytic mechanism of a serine proteinase. A : The OH group o f the catalytic serine becomes polarized as its hydrogen is abstracted by the histidine, which acts as a general base. The aspartate orientates the histidine and renders it a better proton acceptor. The resulting O- group on the serine attacks the carbonyl C atom of the P1 residue. Consequently a tetrahedral intermediate is formed, which is stabilized by the oxyanione hole. B: The histidine now acts like a general acid protonating the future leaving group, the C-terminal part of the substrate. C: The scissile bond has now been cleaved and the Cterminal part of the substrate is released from the active site. D: An incoming water molecule becomes activated by the histidine, which acts as a general base again. The activated water molecule attacks the carbonyl C-atom of the P1 residue, which forms a tetrahedral intermediate that is stabilized by the oxyanione hole. E: Again the histidine acts as a general acid protonating the furture leaving group i.e. the original N-terminal part of the substrate. F: The N-terminal part of the substrate is released from the active site, and the catalytic triad is reestablished and ready for a new round of catalysis.

My first attempt of a scientific cover

cover_crop-01Though it may not look like it, a lot of thought actually went into this design.

The color palette was chosen based on the color scheme PNAS used this “season” (green) exemplified by this mockup of a final cover I did to test how the final product could look like (NB this is not the final version of the actual design):

pnas_cover

Without going into boring details about the project, the major finding  of the paper could be summarized with the word clustering. So I tried to incorporate that into the design (all the light spheres clustering together, plus the molecules clustering together on bacteria surfaces etc.).

Also I didnt want to just use a classic PyMol/Chimera/Qutemol rendered ray-trace image of the molecule in question, as that had been done soooo many times before (and it rarely works). Instead I wanted a conceptual piece with a minimalistic and silhouette-like aesthetic containing no highly detailed three dimensional models, a bit like the visual design from the game limbo.

Anyway in the end it was a no go, but it was fun to do and very educational. It also got me in contact with Yael Fitzpatrick, the former art director of Science, which had some great critique.

16 thoughts on “My PyMol models and figures”

  1. I love your figures, actually using the correct scale. Might be a bit of a silly question but how did you do that? did you just use length say in mm to correspond to length in Å?

    1. Hey Jacob,
      Thank you very much, it is actually not that difficult. Basically you just take one of your models and use that as the ruler so to say. That is, you make sure all other models you want in the same figure are scaled to that single model. I made it easy for myself by loading all the single models I wanted in a figure, into a single PyMol session and then superimposing them all onto the randomly chosen reference model. Dont worry if they superimpose well or not, you just want them to be at the same position in PyMol. By doing this you can simply hide all of the models and the enable one model at the time, export a PNG of it using the same view matrix for all of them. This way they will all be on the same scale. Then you just have to remember to scale them all identically in e.g. photoshop or what ever post processing program you use for generating your final figure. Please feel free to ask all the follow-up questions you want because I am not sure if if I described it clearly enough. Cheers /Ruki

      1. Hi Ruki,

        Thanks so much! I also really like the goodsell render look but no matter what I do in pymol I can’t get it to look as good as your figure, could you give me tips on what you actually modified?

        Many Thanks,

        Jacob

  2. I was wondering if these figures are published or if there is any way these figures (which are amazing) can be replicated elsewhere with all due credit given. Mad props for the work, greetings !

    1. Hi Javier,

      Well some of the figures are published in various scientific papers, but most of them are from my phd thesis on the complement system. Which specific figures are you interested in? no matter what you are allowed to use them if you simply credit the site, then I am happy.

      1. Ruki:

        The one that interests me the most is the one that depicts classical pathway activation, since my Master’s thesis studies just that in the context of a specific adjuvant. I wanted it for my document to have a introductory figure and that gave a good idea of the sizes involved, because pretty much all you can find are stick and ball models that are by no means close to reality. You will be of course be given due credit, and I thank you again for your great work.

        1. I am glad you like them! if you want I could send them to you as a keynote presentation file (NB this requires a mac as converting the file to powerpoint does not look good), that way you will have all the individual molecules and can move them around to create a new figure if you like, or even use them in a talk. If I search deep enough I should be able to find the files in SVG format for inkscape or illustrator as well. Of course this requires that you share your email with me. either way it is up to you. Cheers

          EDIT: Just had a look and I have all of them as SVG (scalable vector graphics) which you can use in Inkscape, which is a free program that is very similar to Adobe illustrator (in case you didn’t know it). The files are on the other hand quite big, so if you are interested I will upload them to my dropbox and share them with you instead. Let me know.

          1. Hi Ruki,
            I have just stumbled upon your art, and it is gorgeous! You are the one that made the figures for that press note from Aarhus, don’t you? Congratulations in your awesome work.

            I need to make a small presentation for one of our colaborators and I was wondering whether I can use your vector figures to show the complement cascade in a different way that we use to see it, with due credit of course.

          2. Hi Rafael,
            Thank you very much!
            I am not sure which release you are referring to, but yes I have made different illustrations, renderings and models for press releases here in Aarhus. If it is specifically the one regarding lectin pathway activation, then yes and it is also published on this site.
            Of course you can use the figures! Are the ones found here on the site suitable? or would you prefer the pathway figures as SVG files so you can move/scale (etc) each molecule around? If yes I can send/share a Dropbox link with you on your registered email. Cheers Ruki

          3. Thank you very much Ruki 😀
            I would like to use the vector files, so that I can just focus on a part of the cascade and play around with the different molecules.
            Cheers!

          4. Well great, I will send you an email with a link or an invitation to share a folder, once I get home as I have all the files on my private desktop.

          5. Dear Ruki:Sorry it took me so long to reply, was immersed in finishing up the thesis itself. For now, the ones in here work amazingly for me, since I need them for the thesis and the final presentation. However, if I ever need a higher res version I will let you know. Thank you so very much for your help and tips !!

      2. Your molecular visualizations are stunning, and although I’m only completing a BSc, more specifically an assignment toward one of my courses I will be using them, and I will certainly be crediting you on them, because they are exquisite!

        Sharon

        1. Hi Sharon,

          Thank you very much, I am glad that you like them! I have many more figures made, I have just not uploaded them, some day maybe.
          Anyway feel free to use as many as you like. Since I did my thesis other structures have been released so it is not 100% up to date anymore. Especially for the Membrane attack complex in the complement system, where many structures have been solved. Also let me know if you would like a link to the dropbox folder where the high-res figures are in. If so I just need your email.
          All the best Ruki

  3. Nice visualisations!
    I am slowly getting into pymol; those bent arrows in
    fig “The lectin activation pathway of the complement system”
    are those done in external program or in pymol?

    Kind regards,
    Pär

    1. Hi Pär,
      Thx! The bent arrows are vector graphic that I put on top of the figures in Inkscape after rendering the molecules in PyMol.
      So no, you can not create these in PyMol, at least not to my knowledge. Let me know if I can help you with anything else

      Cheers
      Ruki

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