Demo of Bio3D
This is a modified version of the Bio3D demo of normal mode analysis. Execute the demo with the commands (in the R console):
library(bio3d)demo(nma)
See also demo(pdb), demo(md), and demo(pca).
- Open R and load library Bio3D
- Download PDB (Lysozyme) and calculate the normal modes
- Print a summary of the modes object
- Plot a summary of the modes object
- Calculate the cross correlation matrix
- Plot the correlation map
- Specify force field 'ANM', and calculate the ANM modes
- Calculate similarity between the C-alpha and ANM force field with RMSIP
- Plot the overlap map resulting in the RMSIP value
- Visualize the first non-trivial mode in PyMoL (vector field representation)
- Vector field representation of the first non-trivial mode
- Make a trajectory of the first non-trivial mode
- Trajectory of mode 7 (first non-trivial mode)
- Ensemble Normal Mode Analysis (of a subset of the kinase superfamiliy)
- Specify PDB identifiers of a set of related protein structures and download these
- Split the PDB files by chain ID
- Sequence and structure alignment with function pdblan()
- Sequence identity of selected structures
- Calculate normal modes of aligned structures
- Print a summary of the ensemble NMA object
- Plot aligned fluctuations
- View mode similarity by RMSIP
- Plot a RMSIP map