A series of steps to create a .x3d file for 3D printing in color using Blender (although many other software can accomplish this, Blender does allow for some flexibility with design)

1. Download the latest version of Blender - https://www.blender.org/
2. Create a new General document
3. Delete all of the objects (press A, X, then enter)
4. Go to the Blender preferences (command-comma) and under add-ons, check the box for "Import-Export: Atomic Blender PDB/XYZ"
5. Then navigate to File->Import->Protein Data Bank (.pdb)
6. Select your .pdb file, choose Mesh for the balls, and either Dupliverts or Normal for the Sticks
   1. A .pdb files can be generated by loading a .cif or .xyz into VESTA and exporting as a .pdb
7. Scale up or down the resolution of the balls and sticks accordingly. Some 3D printing services allow for a maximum number of polygons (e.g. 1,000,000, so the resolution is determined by (number of atoms) * azimuth * zenith + (number of bonds) * sectors < 1,000,000)
   1. Tip: By unchecking the sticks and scaling the Balls to 1.4, more resolution can be obtained by excluding the bonds.
   2. Make sure to choose the appropriate size during the import, it is much easier to rescale here than it will be later
8. Select all (press A), and the Object->Apply->Make Instances Real
9. Object->Show/Hide->Show Hidden Objects
10. Select the Parent balls that have appeared at the origin, and delete them (press X and enter) (there will be as many of these as atom types)
11. Select all and enter Edit Mode (press A then tab, if this doesn't work then click a single atom, press tab, press tab again, then A, then tab - it's a bug in version 2.83)
12. Select None by clicking nothing
13. Select->Select All By Trait->Non Manifold
14. Delete by pressing X then enter (vertices)
15. Press tab to go back to object mode
16. 
17. At this point the model can be freely manipulated: adding more objects to the scene, deleting some atoms, changing the texture of atoms, scaling some atoms up/down in size
18. Select All
19. Right click the model and click Join (in version 2.83 Object->Join doesn't always work, but right clicking and pressing join always works)
20. File->Export->X3D Extensible 3D (.x3d)
21. Colored sandstone 3D printing can be done through https://www.shapeways.com/materials/sandstone, something like this large print would cost a few hundred dollars