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 |
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