Changelog 2.4

bio3d 2.4 Unreleased

Version 2.4, released November 2019, provides a number of new features and enhancements including: new facilities for sequence alignment using the ‘msa’ package from Bioconductor or alternatively using the online server of the European Bioinformatics Institute (EMBL-EBI) (and so a local MUSCLE program is no longer a mandate), a more robust sequence fetching function supporting both the EMBL-EBI and NCBI (National Center for Biotechnology Information) servers, a new function for “core” detection using contact maps, new and improved functions for processing protein structures and doing structural network analysis, and more advanced system environment checking for automatically locating essential external programs.

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: http://thegrantlab.org/bio3d/tutorials/installing-bio3d

Major new/enhanced functions include:

  • seqaln: Supports using ‘msa’ and the EMBL-EBI server to do sequence alignment
  • get.seq: More robust to fetch a large number of sequences and supports EMBL-EBI and NCBI servers
  • atom.select.pdbs: New function for atom selection of a ‘pdbs’ object
  • core.cmap: New function for “core” residues detection using contact maps
  • chain.pdb: Supports inspection on peptide bond (C-N) length
  • community.aln: Comparison of networks with different numbers of nodes
  • dccm.pca, dccm.xyz: Tidier interface by merging “lmi()” and providing a new argument “method”
  • core.find, dccm.nma, dm.xyz, nma.pdbs, pdbaln, pdbsplit, read.fasta.pdb: Improved progress bar
  • dssp.pdb, pdbaln, pymol.dccm, pymol.modes, pymol.pdbs, seqaln: Exefile argument with OS dependent defaults
  • rmsd, seqidentity: More sensible output by fetching row and column names from input

Happy Bio3Ding!