1. Importing a PyMol Structure into Blender

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  • Step 1

Load the PDB file 3IQS into PyMOL. Rename the model to "3IQS_cartoon", hide everything and show the cartoon.

  • Step 2

Save the displayed "3IQS_cartoon" as a VRML file, as shown below:

  • Step 3

Launch Blender (please see link in the Introduction to download and install). Assuming you are looking at the default scene and window layout, press 7 on numeric keypad and the view should change similar to the one below:

  • Step 4

Now select the cube in the center of the screen by right clicking on it, then pressing x and Enter to delete it. This will give you a clean scene to import the protein structure you just exported from PyMOL as VRML 2 (.wrl).

  • Step 5

Now import the "3IQS_cartoon" into Blender by going to "File > Import > X3D & VRML97" as shown below:

  • Step 6

Navigate to the folder where you exported the VRML 2 files from PyMOL and select the "3IQS_cartoon" file:


Click the "Import X3D/VRML97" button after selecting the correct file and just click "OK" if a dialog comes up.

  • Step 8

Doing the above should result in a display such as the one below: