Bio3D version 2.3

We are excited to announce the release of version 2.3 of Bio3D. This release contains several new functions and important improvements to existing code and documentation.

For a fine-grained list of changes or to report a bug, consult:

Download Bio3D version 2.3-0

Bio3D on CRAN

Bio3D is now on CRAN, and can be installed with the command

install.packages("bio3d", dependencies=TRUE)

from within an R session.

Vignette updates

  • Installing Bio3D ( PDF | HTML )
  • Getting started with Bio3D ( HTML )
  • Beginning Structure Analysis with Bio3D ( PDF | HTML)
  • Beginning Trajectory Analysis with Bio3D ( PDF | HTML)
  • Enhanced Methods for Normal Mode Analysis with Bio3D ( PDF | HTML )
  • Comparative sequence and structure analysis with Bio3D ( PDF | HTML )
  • Introduction to Correlation Network Analysis with Bio3D ( PDF | HTML )

Major new/enhanced functions since version 2.2

  • aanma (aanma.pdbs) Normal mode analysis with all-atom elastic network model
  • gnm (gnm.pdbs, dccm.gnm) Normal mode analysis with Gaussian network model
  • 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 Build a pymol session from a 'pdbs' object
  • read.cif Read a Protein Data Bank (mmCIF) coordinate file
  • read.crd Read a CHARMM CARD (CRD) or AMBER coordinate file
  • read.prmtop Read parameter and topology data from an AMBER PrmTop file
  • plot.matrix.loadings For plotting loadings obtained from pca.array
  • community.aln Align communities from two or more related networks
  • read.pdb Use Rcpp to (more rapidly) read and parse PDB files. (Old function is renamed to read.pdb2)
  • Support 'insert' identifier
  • vmd.cna (vmd.cnapath) Renamed view.cna (view.cnapath)
  • pymol.dccm (pymol.modes, pymol.nma, pymol.pca) Renamed "" functions
  • plot.fasta Improved plotting function for multiple sequence alignment
  • read.mol2 (write.mol2,, trim.mol2, as.pdb.mol2) Read, write and manipulate mol2 files