bio3d 2.3 Unreleased

Version 2.3, released September 2016, provides a number of new features and enhancements including: new facilities for ensemble normal mode analysis (NMA) with all-atom elastic network model (ENM) and Gaussian network model (GNM), enhanced NMA calculations with the rotation-translation block (RTB) method, new “4-bead” coarse-grained ENM, more efficient reading of large PDB files using Rcpp, PDB annotation from the PFAM database, and more supported I/O file formats.

We have also updated online vignettes and other documentations. For a fine-grained list of changes, or to report a bug, please consult:

For full install instructions see:

Major new/enhanced functions include:

  • aanma: All-atom ENM normal mode analysis (with RTB and 4-bead ENM supported)
  • aanma.pdbs: Ensemble NMA with all-atom ENM
  • gnm: Gaussian network model (GNM) calculations
  • gnm.pdbs: Ensemble NMA with GNM
  • dccm.gnm: Dynamical cross-correlation for GNM
  • pdbs2sse: Retrieve SSE from pdbs object with appropriate residue numbers for plotting
  • mask.dccm: Produce a new DCCM object with selected atoms masked
  • pdb.pfam: Function for PFAM annotation of PDB IDs
  • pymol.pdbs: Builds a pymol session from a ‘pdbs’ object
  • read.cif: Read a Protein Data Bank (mmCIF) coordinate file
  • read.dssp: For reading existing DSSP output files
  • read.stride: For reading existing STRIDE output files
  • read.crd: Read a CHARMM CARD (CRD) or AMBER coordinate file
  • read.prmtop: Read parameter and topology data from an AMBER PrmTop file
  • read.pdb: Use Rcpp to (more rapidly) read and parse PDB files
  • read.pdb2: Renamed old read.pdb function
  • plot.matrix.loadings: For plotting loadings obtained from pca.array()
  • community.aln: To align communities from two or more related networks
  • Supports ‘insert’ identifier
  • vmd.cna and vmd.cnapath: Renamed view.cna and view.cnapath
  • pymol.dccm, pymol.modes, pymol.nma, and pymol.pca: Renamed functions
  • plot.fasta: Improved plotting function for multiple sequence alignment
  • read.mol2, write.mol2,, trim, as.pdb: Read, write and manipulate mol2 files with functions

Happy Bio3Ding!