2. PyMol and ChimeraX

There are several ways to import protein structures into Blender and other 3D programs for animation and rendering, they all have their advantages and disadvantages. In this section we will cover how to export a 3D model from PyMol or ChimeraX (the principle remains the same for other Molecular Graphics Software) and to then import it into Blender.

Exporting the Model

PyMol

fetch 4ozs

If we run the following command inside of PyMol, we get some information on the save command and the formats that we can save in:

help save

DESCRIPTION
 
    "save" writes content to a file.
 
USAGE
 
    save filename [, selection [, state [, format ]]]
 
ARGUMENTS
 
    filename = string: file path to be written
 
    selection = string: atoms to save {default: (all)}
 
    state = integer: state to save {default: -1 (current state)}
 
PYMOL API
 
    cmd.save(string file, string selection, int state, string format)
 
NOTES
 
    The file format is automatically chosen if the extesion is one of
    the supported output formats: pdb, pqr, mol, sdf, pkl, pkla, mmd, out,
    dat, mmod, cif, pov, png, pse, psw, aln, fasta, obj, mtl, wrl, dae, idtf,
    or mol2.
 
    If the file format is not recognized, then a PDB file is written
    by default.
 
    For molecular files and where applicable and supported:
 
    * if state = -1 (default), then only the current state is written.
 
    * if state = 0, then a multi-state output file is written.
 
SEE ALSO
 
    load, get_model
 

Inside of the nodes, we see the supported output formats are: pdb, pqr, mol, sdf, pkl, pkla, mmd, out, dat, mmod, cif, pov, png, pse, psw, aln, fasta, obj, mtl, wrl, dae, idtf, or mol2.

Some of these are relevant to the work that you are likely already familiar with such as the .mol and the .pdb, but a lot of them may seem strange. .obj, .dae, .wrl are all generic 3D model formats that are not specific to proteins at all. You can save your 3D model you have displayed inside of your viewport with the following command:

save protein.wrl

Different 3D model formats have pros and cons. I have found .wrl to be the best when exporting from PyMol.

PyMol will export the 3D model relative to where the camera currently is. That means if you export one half a dimer, move the camera, then export the other half of the dimer, they will not line up when importing to Blender.

You should now have a 3D model save in your working directory, which is ready to be imported into Blender.