Tetrahedral Meshing for Ribosome

Figure 1: Small subunit (30S), residue level with blobbyness -5.0 (1J5E_low_5.0). Middle – interior mesh with 360715 vertices, 1790029 elements and 1035 (0.0578%) bad elements; Right – exterior mesh with 325821 vertices, 1590203 elements and 1500 (0.0943%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

Figure 2: Small subunit (30S), residue level with blobbyness -0.5 (1J5E_low_0.5). Middle – interior mesh with 182937 vertices, 900679 elements and 291 (0.0323%) bad elements; Right – exterior mesh with 201334 vertices, 1010060 elements and 408 (0.0404%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

Figure 3: Small subunit (30S), atomic level with blobbyness -5.0 (1J5E_high_5.0). Middle – interior mesh with 380711 vertices, 1505616 elements and 1080 (0.0717%) bad elements; Right – exterior mesh with 505628 vertices, 2377356 elements and 3559 (0.1497%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

Figure 4: Big subunit (50S), residue level with blobbyness -5.0 (1JJ2_low_5.0). Middle – interior mesh with 534188 vertices, 2668742 elements and 1767 (0.0662%) bad elements; Right – exterior mesh with 438174 vertices, 2090789 elements and 2231 (0.1067%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

Figure 5: Big subunit (50S), residue level with blobbyness -0.5 (1JJ2_low_0.5). Middle – interior mesh with 222675 vertices, 1095441 elements and 278 (0.0254%) bad elements; Right – exterior tetrahedral mesh with 235318 vertices, 1172859 elements and 485 (0.0414%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

Figure 6: Big subunit (50S), atomic level with blobbyness -5.0 (1JJ2_high_5.0). Middle – interior mesh with 615424 vertices, 2408676 elements and 1248 (0.0518%) bad elements; Right – exterior mesh with 553412 vertices, 2457534 elements and 5024 (0.2044%) bad elements. All bad elements are removed using the edge contraction and smoothing method.

References:

1. Y. Zhang, C. Bajaj, B-S. Sohn. 3D Finite Element Meshing from Imaging Data. Submitted to the special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 2003.

2. Y. Zhang, C. Bajaj, B-S. Sohn. Adaptive and Quality 3D Meshing from Imaging Data. Proceedings of 8th ACM Symposium on Solid Modeling and Applications, pp. 286-291. Seattle, WA. June 16-20, 2003.

* bad element: the element satisfying Joe-Liu parameter < 0.01.