| Features added after the publication of the paper | |
| Generate crystal unit cell, biological dimer from asymmetric unit | |
| Cluster and subcluster based on input data (e.g., Tanimoto similarity matrix) | |
| Separate a GCE trajectory into Amber trajectories | Extract cluster center structures after clustering |
| Read charges from Charmm or Amber topology file or Autodock .pdbqt file | |
| Calculate and plot the difference between residue distance matrices and residue RMSFs | |
| Calculate and plot the difference between bond (hydrogen/hydrophobic bond; salt bridge) matrices | |
| Individualize atom names, scale coordinates, save mol2 file with names or coordinates changed | |
| Allow atom selection by atom or residue names; generate plot of atom-atom distance SDs | |
| Support for Tripos .mol2 (mostly for input) and Maestro .mae (only for input) formats | |
| Rotate a molecule based on a bond direction | Calculate intermolecular distance matrix |
| Concatenate atom-atom bond histories to residue-residue bond histories | |
| Calculate bond state statistics and autocorrelations | Draw bonds between (anti)correlated bonds |
| Heuristic clustering into cliques | Density-based clusterings |
| Helix analysis (TRAJHELIX) on several helices | Filter solvents by proximity, CV or interface |
| Align a molecule's principal axes to the XYZ axes | Calculate angle distributions with dial plots |
| Calculate two kinds of helix-helix distances, and helix rotations relative to other helices | |
| Filter for solvents forming H-bond bridges | Bond tracks for mutually proximal atom pairs |
| Residue-residue autocorrelation (lifetime) | Swap chirality |
| Input of PDBx/mmCIF files | Convert sequence files |
| Read bond list from RTF or top files; print MMC MAKB or PDB CONECT records | |
| Specify atom lists for molecular overlay | Filter trajectories/structures for energy |
| Plot and cluster torsion angle circular correlation matrix, calculate its eigenvectors, eigenvalues | |
| Create a PDB file of a rectangle (box/cube) | Calculate RMSD for residues |
| Process clusters with user-defined limits; use even-spaced or random intial trys for clustering | |
| Create periodic replica cells | Plot PBC cell sizes, volume |
| Track solvent diffusion, membrane transit | Principal axes by domains, angle between them |
| Average data in 1D plots | Calculate membrane deviation from flatness |
| Inertia plot for K-means and K-medoid clustering | Helix property tables, correlation, NMA |
| Spearman and Kendall Tau rank correlations too | Translate while converting a trajectory |
| Option to permute bond list from topology files | Option to override Y axis scale in 1D plots |
| Check for long/short bonds in a trajectory | Check for unphysical features on a trajectory |
| Check for ligand-ligand overlap | >Calculate SD corresponding to CV values |
| Calculate orientational fluctuation of a domain | Color code bond tracks by domains |
| Change a dihedral angle | Secondary structure segment and residue counts |
| Translate/rotate individual molecules | Enhanced selection for bond plots |
| Rotate around an axis defined by two atoms | Shift in a direction defined by two atoms |
| Calculate intra molecular RMSD | |