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Bio3D version 2.2

We are excited to announce the release of version 2.2 of Bio3D. This release contains several new functions and important improvements to existing code and documentation.

Note important bugfix related to function atom.select() released with version 2.2-2 (March 2 2015).

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

Download Bio3D version 2.2-2

Bio3D v2.2-2 (source)

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 )
  • NEW: 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 )

New functions since version 2.1

PDB related

  • clean.pdb function for producing 'cleaned' PDB objects
  • biounit construct the biological unit
  • cat.pdb to combine two or more PDB files
  • as.pdb to build a PDB object from vectors
  • ATOM.only option in read.pdb(), store all info including REMARK in 'pdb' if ATOM.only=FALSE
  • basename.pdb simple utility function for simplifying working with PDB file names

Various updates

  • aa.table data file for amino acids mass and 3:1 name conversion
  • s3 generic functions for pdbfit, core.find, and geostas
  • plot and print geostas results
  • Provide mass weighting option in pca.xyz()
  • New improved plot.cmap() function
  • Sub-optimal path analysis in correlation networks function cnapath
  • General atom.select() improvements. Including implementing more keywords and speed improvements
  • Spline option in view.cnapath() to draw all paths explicitly
  • Improvement of is.gap() function for matrix/alignment/vector TRUE/FALSE gap inspection (a more simple approach to using gap.inspect()
  • Improvement of plot.pca() allowing PC1-PC2 and overview plot with better annotation
  • Improvements to plot.bio3d() SSE annotation for added robustness with multi-chain systems
  • Add SSE storage to read.fasta.pdb()
  • Add conservation line to output of print.fasta()