Fig. 5: Vibrations of the dilated human Nuclear Pore Complex (NPC).
From: Scalable computation of anisotropic vibrations for large macromolecular assemblies
Overview of motions in several representative non-zero modes. a The first non-zero normal mode (indexed as Mode 0) (b) the third non-zero normal mode (indexed as Mode 2) (c) clipped view of the fifteenth non-zero normal mode (indexed as Mode 14) (d) bird-eye view of the fifteenth non-zero normal mode (indexed as Mode 14) The arrows in magenta indicate an average directions for the local clusters of the displacement field, while the tiny black arrows show more detailed displacement fields of 10,000 atoms randomly chosen from those in the top 80% quantile of vibration magnitude in the eigenvector. Color scale in the cartoon from blue to red indicates increasing magnitude of vibration. Note that a logistic kernel is applied to the eigenvector to control the magnitude in visualization. (See “Methods”). e The first 30 non-zero eigenfrequencies of the macromolecule, the eigenfrequency is the square root of eigenvalue \(\omega\). The black arrows indicate the first non-zero eigenmode displayed in (a), (b), (c) and (d). Source data are provided as a Source Data file.
