Whats New

New features and bug fixes of the latest release of the bio3d package are listed here. For more general information see the package homepage and online documentation.

Whats New Version 1.0-4 (May 07) Additions since last release Version 1.0-3 (Nov 06) Additions since last release Version 1.0-2 Additions since last release Version 1.0-1 Fist released version

Version 1.0-4 (May 07)

Additions since last release

New Functions:

Function Name:	Description:
aln2html	Create a HTML Page For a Given Alignment
plot.bio3d	Plots with marginal SSE annotation
conserv	Score Residue Conservation At Each Position in an Alignment
seqaln.pair	Pairwise Alignment of Identical Protein Sequences

The function dssp has a new input paramater (resno=TRUE) to give output in terms of residue numbers and optionaly, when FALSE, in terms of residue index (position in sequence).
The function read.fasta has been completely re-writen.
A new package manual in PDF format is available for download

Version 1.0-3 (Nov 06)

Additions since last release

New Functions:

Function Name:	Description:
torsion.pdb	Calculate Mainchain and Sidechain Torsion/Dihedral Angles
torsion.xyz	Calculate Torsion/Dihedral Angles
pca.tor	Principal components analysis (PCA) on torsion angle data
pca.project	Project Data onto Principal Components
wrap.tor	Wrap Torsion Angle Data
aa.index	AAindex: Amino Acid Index Database
aa2index	Converts sequences to aminoacid indeces from the AAindex database
angle.xyz	A function for basic bound angle determination

Version 1.0-2

Additions since last release

New Functions:

Function Name:	Description:
read.crd	Read a CHARMM CRD Format Coordinate File
write.crd	Write a CHARMM CRD Format Coordinate File
dssp	Secondary Structure Analysis with DSSP
stride	Secondary Structure Analysis with STRIDE
rmsf	Atomic RMS Fluctuations
seqaln	Sequence Alignment
ide.filter	Percent Identity Filter
rmsd.filter	RMSD Filter
seqbind	Combine Sequences by Rows Without Recycling
unbound	Sequence Generation from a Bounds Vector
convert.pdb	Convert between CHARMM, Amber, Gromacs and Brookhaven PDB formats
atom2xyz	Convert Between atom and xyz Indices
wiki.tbl	WIKI Table

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Version 1.0-1

Fist released version

Functions include:

Function Name:	Description:
aa123	Convert Between 1-letter and 3-letter Aminoacid Codes
aa321	Convert Between 1-letter and 3-letter Aminoacid Codes
aln	Bio3d Example Data
atom.select	Atom Selection From PDB Structure
bio3d	Biological Structure Analysis
bio3d-package	Biological Structure Analysis
bounds	Bounds of a Numeric Vector
bwr.colors	Color Palettes
consensus	Sequence Consensus for an Alignment
core	Bio3d Example Data
core.find	Identification of Invariant Core Positions
dm	Distance Matrix Analysis
entropy	Shannon Entropy Score
fit.xyz	Coordinate Superposition
gap.inspect	Alignment Gap Summary
identity	Percent Identity
kinesin	Bio3d Example Data
lbio3d	List all Functions in the bio3d Package
mktrj.pca	PCA Atomic Displacement Trajectory
mono.colors	Color Palettes
orient.pdb	Orient a PDB Structure
pairwise	Pair Indices
pc.xray	Bio3d Example Data
pca.xyz	Principal Component Analysis
pdb.summary	Atom Selection From PDB Structure
pdbs	Bio3d Example Data
plot.core	Plot Core Fitting Progress
plot.dmat	Plot Distance Matrix
plot.pca	Plot PCA Results
plot.pca.loadings	Plot Residue Loadings along PC1 to PC3
plot.pca.score	Plot PCA Results
plot.pca.scree	Plot PCA Results
read.dcd	Read CHARMM/X-PLOR/NAMD Binary DCD files
read.fasta	Read FASTA formated Sequences
read.fasta.pdb	Read Aligned Structure Data
read.pdb	Read PDB File
rmsd	Root Mean Square Deviation
rot.lsq	Coordinate Superposition
write.fasta	Write FASTA Formated Sequences
write.pdb	Write PDB Format Coordinate File
xyz	Bio3d Example Data

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