Quick and easy animated pictures of proteins

So, here is an imaginary situation. You have a deadline to achieve and have minimal internet to reach the goal. Few hours before the deadline, your PI asks if you can send him a movie of the protein of interest in PyMOL. He specifies that the movie show the protein rotating, the active site and the ligand bound with it in surface representation, ligands as ball-and-stick, etc. He has a grant review presentation tomorrow and needs it asap.

You finish the movie and realize that to make a good impression one would need a high quality movie and that is going to eat up your internet time in uploading and you may end up not achieving both (Yours and your PI’s) goals.

Ta da! That’s where you need POLYVIEW-3D.

  • It is quick and easy to use
  • Easy interface with no complex manuvering required.
  • Best part are the animated gifs, that are easy to send via email.
  • You can set an orientation using the Jmol java applet.
  • You can choose either RasMol or PyMOL rendering
  • From tiny images (50×50 pixels for lab webpages) to large sized pictures (1000×1000 pixels for presentations)
  • PNG and TIF format for static images. Animated ones are (of course) in Gif format.

Some of the images I made using this web-server



One chain in surface colored w.r.t hydrophilicity and another in Cartoon colored w.r.t secondary structure, with halo lighting


One chain in surface colored w.r.t hydrophilicity and another in Cartoon colored w.r.t secondary structure, without halo lighting


Chain A showing the active site, with ligand bound. The residues interacting with ligand are colored blue. Only one ligand, the other one is from chain B.


Same as above, with animation.

I think this cool, give it a try!


ResearchBlogging.orgPorollo, A., & Meller, J. (2007). Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D BMC Bioinformatics, 8 (1) DOI: 10.1186/1471-2105-8-316

  1. Ivan said:

    Can I use the animations in a biology-themed game I’m programming! Thank you!

    • ragothamanyennamalli said:

      Of Course, you are welcome to share the images I created for this post. Biology themed game sounds exciting! Please keep me posted!

  2. Hi,
    May I use one of the GIF’s for a website? How should I cite it?

    Thank you!

    • ragothamanyennamalli said:

      Thanks! You can cite the blog itself, along with the tool that was used to make the gif. 🙂

  3. himaja said:

    how do you set these molecule rotation
    i am not able to get it
    what is the input command given for the molecules to rotate?

    • ragothamanyennamalli said:

      Under “Image Settings” change the “Type of Request” to Animation, and that enables the “Animation settings” tab and only after you click Submit, one sees the final animated image and not in the preview.

      • himaja said:

        sir i like to know how did you do this animation i have the structure but i dont know how to do this animation.
        You are telling image settings….. may i know which software or website you mean.
        thank you very much for your quick reply
        nice blog

      • ragothamanyennamalli said:

        Use the polyview-3D website, which is what the blogpost is about.

  4. himaja said:

    Sir may i know how to download the animated structure after submitting it?

    • ragothamanyennamalli said:

      Right click and save as.

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