Download

Before you attempt to install Bio3D you should have a relatively recent version of R installed and working on your system. Detailed instructions for obtaining and installing R on various platforms can be found on the R home page. 

Obtaining Bio3D

The Bio3D package can be most easily obtained and installed via CRAN. Start R by issuing the command R and then from the R prompt install the Bio3D package:

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

See the Installing Bio3D vignette for addational instructions along with details of various utility packages and programs that will either interface directly with Bio3D (MUSCLE, DSSP and STRIDE), or that we consider generally invaluable for working with biomolecular structure and sequence data (e.g. VMD, PyMOL, and SEAVIEW).

Older Versions

Older versions of the package can also be obtained. Changes between versions are documented on this site along with a description of Utility programs that may prove useful.

Development Version

For the majority of users we recommend the use of the last stable release available from CRAN. The development version is available from our bitbucket repository and typically contains new functions and bug fixes that have not yet been incorporated into the latest stable release.

There are several ways to download and install the development version of Bio3D. The simplest method is to install directly from our bitbucket repository using the R function install_bitbucket() from the devtools package.

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/") 

Alternative installation methods and additional instructions are posted to the wiki section of our bitbucket repository.  

Where Next

For an introduction to working with bio3d and the R enviroment see the User guide. A number of worked examples are available as short Tutorials. You can also view the online Documentation.