This image is generated from a .pdb of Acetyl Coenzyme A.
Before I get too excited about creating my own quantum level interface to matter in blender it makes sense to see what is already done. Dr. Clemens Barth of the CINaM was so kind as to create a pdb tool for blender. The usage page for Atomic_Blender has documentation on how it is applied. It is accessed from the physics panel ( that seems pretty fitting ) [ If only they had a chemistry panel :) ] of a scene and I noticed a few glitches when using files from the archives, ( which will open and be displayed with PyMol ) which have to do with the extraneous information that is included in the files. The columns in a pdb file seem to be poorly documented, but I will have to look at the spec to be sure.
I am guessing I could snarf a lot of file technique from PyMol and integrate it. I am doing the "quantum" level physics of the atoms , which includes the nucleus down to its sub parts. I put quantum in quotes, because it is just the shadow of what is taking place. It is vastly more complex, and on top of that it is almost impossible to represent in a form that looks like anything. I am using color and intensity, along with normals and scale to represent the 6 dimensions and 3 space ( 3 way ) vectors that are involved as well as the n-dimensional space forms. Just the representation of Hydrogen requires going down those twisty little passages that all look alike , into time and anti-time, while dropping objects so I can find my way back.
ADDED PARAGRAPH:I started looking at PyMol and I am confused , as it is an "open source closed source??". Whatever. I did "apt-get source rasmol" to get rasmol source in "c", which works just as well and am looking at the methods there. I have a pdb viewer that I wrote for my program, and along with the blender pdb, wxpython, and rasmol, should have something better than their free but not program. I am implementing quantum level effects of emitted and absorbed radiation as well as the temporal2 electromagnetic fields. Pretty pictures are entertaining for a while, but I wanted to use it to construct new molecules and predict shape, catalytic activity, bond lengths, spectra, and reactions as well as its reaction to conditions like absolute zero or at least the point of superconducting effect for those that exhibit that state. I suppose it matters not where I start, as most of it is new. I wonder if I can display the molecules with their emission spectrum cues. I suppose I could color the ball with texture instead of a single color and that way I could embed the symbol in the texture as well, just for grins. I could make several textures actually that are generated from spectrum as well as electron affinity, ionization potential, and other properties. I am beginning to suspect that some of the long standing principles of describing and modeling atom systems may be wrong in a serious way. It is just a strong suspicion at the moment, but my completed model should remove all doubt.
The integration of features in blender is coming along nicely and I thank the blender gurus for that. They have really done some good work.
I was thinking about people in space and it seems to me that I would start with inertial canceling as well as something equivalent to the fictional "General Products Hull" of the Puppeteers. It is theoretically possible IMHO, though very involved to implement. But then I suppose the first Roman slave ships didn't have a multimedia room for passengers.