Mesh proteins: the quest continues

You may recall that I made some mesh proteins and other biological structures in SL in the very early days following the release of mesh. I'm now trying to improve the process but it is far from simple.

The ribbon-like structures you can see above represent the A chain of cholera toxin [PDB: 1xtc] in cartoon format as exported from UCSF Chimera. The more bulky structure is a surface model for the entire toxin. You will note that some of the ribbon structures appear latticed. These were exported from Chimera in X3D format. By contrast, exporting in stl format preserves the cartoon structure intact (an improvement). In both cases the structures were further processed in MeshLab (using Quadric Edge Collapse Decimation) to reduce the face count to 20000 and convert the structure to dae (COLLADA) format. So far so good. (updated 7 Jan 2012 for latest Chimera version).

The problem comes when you try to generate a UV map to colour the three different structure types. I've tried a couple of approaches. Firstly, I broke the molecule into parts in Chimera and exported the three parts separately before colouring them inworld and attempting to put them back together (structure in background). Notionally that is very simple but in practice it had me going goggle-eyed, even with the white template structure to work from.

The second approach involved "painting" the molecule using one or more packages designed for the purpose. Again, using the obj format file seemed best in terms of compatibility. Thus far the packages that look most hopeful are 3DCoat (trial version) and the free version of BlackSmith3D. While the former appears much easier to use, the latter works OK too and I was able to generate and export a painted UV map from it. The problem I am now faced with, however, is aligning the texture on the mesh. The structure at the front right should be mostly red with a few green splodges (it's just a test); it's mainly splodges.

It may sound odd given the distressed image above (and do click through for detail) but I'm actually quite pleased with this progress, albeit that there's every chance I'm missing more obvious solutions (do tell!). At the moment I run OpenSim 0.7.2 as Sim-on-a-Stick, upload the mesh using SL Viewer 3 and use Dolphin 3 for viewing.