Blender in visualization of molecules

17 Oct

Yes, you can use Blender to prepare figures for your next paper and the results for sure will look different than the ones obtained with a standard software (hemoglobin [1HBG] as example below)… But given amount of work and really steep learning curve (at least for somebody who tries that for the very first time), I would not recommend Blender that much… 🙂


UPDATE: if you look for a way to import a PDB file into Blender, some instructions are at the bottom of this page.


Posted by on October 17, 2007 in Software, Visualization


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10 responses to “Blender in visualization of molecules

  1. Deepak

    October 18, 2007 at 06:44

    That’s a neat figure. A lot of the figures in my PhD thesis were done in FormZ .. definitely made a difference

  2. freesci

    October 18, 2007 at 06:51

    Thanks Deepak.

    FormZ? I didn’t have a chance to try, but its interface looks way cleaner than Blender’s. Can you share some details (like how to get PDB file inside; I’ve spent more time on importing the structure than on rendering)?

  3. Pedro Beltrao

    October 18, 2007 at 15:46

    Lights,camera,action ! Once upon a time there lived an hemoglobin in a land called far far way :).

  4. Deepak

    October 18, 2007 at 20:44

    This was a very long time ago … and I didn’t do the images, my wife did.

    What I did was open up the structures in a visualizer capable of VRML export. The VRML was then imported into FormZ and material, shadows, shapes, etc were added there. Cool applications – rendering a proton channel, showing off potential ion binding sites, etc.

  5. freesci

    October 20, 2007 at 15:36

    Thanks Deepak, I did try VRML, however Blender understands only version 1.0… Will look further.

    Pedro, if you have a scenario I can start rendering next pictures 🙂 . I’m not into animations, but a comic? Why not? 🙂

  6. Monica

    January 8, 2009 at 12:42

    I don’t know if anybody is still interested, but we have developed a tool for importing pdb files in Blender, and also for animating transitions among different conformations, if you have a file NMR that contains more than one.
    Want to try?
    Just go to our website and download the scripts. There is also a paper on our site, and on the Blender site, you can see a conference in which i describe a little in more details our work.

    Will be pleased to know your comments, thanx,

  7. Pawel Szczesny

    January 8, 2009 at 12:57

    Monica, thank you. Your work is really impressive (ATP had blown me away). I’ll sent address of your page around – there are few people interested.

    Unfortunately, I’m blind or not caffeinated enough, because I cannot find any “download” link for your scripts. Can you point me to them?

  8. nah sivar

    February 14, 2009 at 14:33

    Monica, could you point us to the URL / Download Link ?

    Also a general purpose tutorial (basic to advanced , of how to start with a PDB file , go & create such beautiful images), will be great
    along with a consolidated post of all the other such tools (with not so steep learning curve ) will be helpful

  9. nah sivar

    February 14, 2009 at 17:24

    Could you provide pointers (or tutorials) to get one started with playing with PDB in Blender?

    it will be nice if the importing of pdb, & doing things with it is presented for someone really new to Blender.

    akin to starting with Blender by playing with PDB strcutures ?!

    someone plz.,

  10. Monica

    August 3, 2009 at 10:18

    Hi everyone!!,
    sorry I never came back to reply. We are restructuring our website, so please email me for blender scripts to do protien work. Although somebasic features are will defined, the major aim of our work is to have proteins moving, as in animation, but based on biological dataset.
    This is not fully adjusted yet (it is difficult!), but as soon as we have it all set, we will:
    post it everywhere
    record a tutorial
    be open for further developments

    Thanks for your interest, and just mail me if you want the scripts.


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