I’ve finished the new animatic, so I will be showing this to Angus at the next possible opportunity. I’m still unclear on the shape of p19 (sadly couldn’t find the whole molecule on the PDB, just various individual amino acid chains) or the identity of the other tumour-suppressor proteins involved, so hopefully I will get some answers to these questions at the next meeting.
This is the reel of scientific visualisation company XVIVO, who produce work for all kinds of sectors from educational to commercial to entertainment. It’s fun watching the reel and trying to figure out which sector each animation was created for.
Aside from thinking up alliterative post titles, I have been investigating a plug-in called Molecular Maya (mMaya for short). Having spent numerous frustrating weeks trying to find visual reference for some of these molecules, the discovery of mMaya and the Protein Data Bank (PDB) has been a godsend. Not only can I now find visual reference of proteins on the PDB, I can download Maya models of them!
The downloaded data comes in the form of a .pdb file, which appears to be a group containing smaller groups called “chains,” which contain various particle objects, curves, and an nSolver, which I presume is what drives the vast number of different display options I can choose for the object.
The most important feature in my eyes is the ability to drape a mesh onto it to create a more appealing model. There are various options to tweak this too: in the video below, I have been experimenting with the presets for “high” fidelity (left) and “medium” fidelity (right).
One slight drawback is that the default assigned shaders are… a little garish, so I replaced them with misss_fast_skin shaders. Another drawback is that the mesh (particularly in the case of the “High” mesh) is extremely high-poly, so it has to be Reduced if Maya isn’t to crash. Also, the mesh is always triangular, and there doesn’t seem to be any option to make a quadrangular mesh instead. So I’m now fiddling with Maya’s Quadrangulate function, with… mixed results.
Still, I’m really glad that I found it. The PDB files can be used freely (though citation of the original authors is encouraged). I’m not sure whether I’d be allowed to use them for my project, so I’ll have to check with my supervisor. If I can insert mMaya into my pipeline, I’ll be able to spend more time on the more complex modelling challenges such as the nuclear envelope and chromatin.
Cell Shading 