VTK PolyData Details

The VTK exporter in Chimera and ChimeraX (used by the ChimeraX save command) was contributed by Shawn Waldon as part of the SketchBio project in 2013. It exports molecular structures and surfaces, not density maps, to an ascii legacy VTK file format [documentation PDF]. For molecular structures, it exports points and lines for the atoms and bonds, and for surfaces it exports a mesh. At each point (atoms and surface), it exports attributes of the associated atom: modelNum, atomNum, resType, resNum, atomType, bFactor, occupancy, and chainPosition.

• modelNum, atomNum, and resNum are integer indices starting with 0. Models are numbered 0,1,2... sequentially (not using the ChimeraX model ID), and the atom and residue indices are positions in the lists of all atoms and all residues per model, respectively.
• atomType and resType refer to the ChimeraX atom name and residue name, e.g., CA and TRP
• chainPosition is the residue index in a chain (starting with 0) divided by the number of residues in that chain