- Quick view of large trajectory (DCD) files
- Preparing a protein-only DCD file (removing waters)
- Removing global rotations-translations from a protein-only DCD file
- Removing global rotations-translations using selected atoms for fitting
- Calculation of rmsd from the starting structure
- Calculation of the average structure and corresponding fluctuations
- Calculation of rmsd from the average structure
- Calculation of the evolution of the radius of gyration
- Calculation of the average Cα-Cα distance map and the corresponding rmsd
- Calculation of frame-to-frame rmsds
- Variance-covariance and cross-correlation analysis
- Variance-covariance analysis and comparison with experimental results
- Principal component analysis
- Calculation of eigenvalues and eigenvectors
- More on eigenvectors and eigenvalues
- Eigenvectors and eigenvalues, sufficient sampling issues
- Comparison of sets of eigenvectors
- φ,ψ time series
- χ-value analysis (including χ1-χ2 plots and residence times)
- Cluster analysis of trajectories
- Secondary structure analysis of protein trajectories
- Anisotropic fluctuations (and their visualisation)
- Calculation of water and ion distributions