Bio3D_install.RmdOn all platforms (Mac, Linux, and PC) open R (version 3.1.0 or higher) and use the function install.packages() at the R command prompt to install the package from your local CRAN site:
install.packages("bio3d", dependencies=TRUE)
Alternatively, if you prefer to use RStudio, select Tools \(\rightarrow\) Install Packages.., Enter bio3d in the Packages text box (and make sure Install Dependencies is selected). Then click Install.
For full Bio3D functionality you should have MUSCLE, DSSP, and NetCDF (headers and libraries) installed on your system and in the search path for executables. Background details and install instructions for each of these packages on different operating systems is provided further below.
You should now be able to load the Bio3D package into your current R session by typing the usual library(bio3d) command at the R Console.
We now suggest you use the command demo("pdb"), demo("pca") and demo("md") to get a quick feel for some of the tasks that we will be introducing in subsequent vignettes:
Before you attempt to install Bio3D you should have a relatively recent version of R installed and working on your system (we recommend at least R version 3.1.0). Detailed instructions for obtaining and installing R on various platforms can be found on the R home page http://www.r-project.org.
Bio3D makes use of a number of additional R packages including ncdf, bigmemory, XML, RCurl and igraph. Make sure required headers and libraries are installed on your system prior to installing these R packages. i.e. the R package ncdf requires netcdf and libnetcdf-dev; XML requires libxml2-dev; and RCurl requires libcurl3-dev.
In addition, for full Bio3D functionality you should have MUSCLE and DSSP installed on your system and in the search path for executables.
Note: If you encounter difficulties in installing any of the suggested packages, note that most functions in Bio3D will work just fine without. e.g. ncdf is only required for reading/writing netcdf binary trajectory files; igraph for visualization of correlation network analysis; RCurl and XML for searching and fetching data from various biomolecular databases.
The Bio3D package is available in two forms from CRAN and the Bio3D website1
as platform independent source code (intended primarily for Mac and Unix systems),
To install from source requires that your machine has standard compilers and tools such as Perl 5.004 or later. If you run into problems with source installation please refer to section 6.1 of the R Installation and Administration Manual. Below we provide installation instructions for some of the most common OS’s.
R on Mac OS X can be used either on the command-line, like on other UNIX systems, via the R.app GUI (included with your binary R install), or the increasingly popular RStudio IDE.
Regardless of your preferred interface you should be able to find the R command prompt and install the Bio3D package from CRAN using the following command:
install.packages("bio3d", dependencies=TRUE)
We recommend using the homebrew package manager for installation of MUSCLE, DSSP and NetCDF. For more information on homebrew see http://brew.sh/index.html. Using homebrew these packages can be installed with the following command:
brew install homebrew/science/muscle
brew install homebrew/science/netcdf
brew install homebrew/science/dsspAlternatively, you can use the Packages and Data menu of the R.app GUI, in particular the sub-item Package Installer: Download the source tar.gz file from above. In the R GUI select Packages and Data \(\rightarrow\) Package Installer \(\rightarrow\) Local Source Package, and press the Install button. Select the Bio3D tar file and press Open.
In RStudio, select Tools \(\rightarrow\) Install Packages.., Enter bio3d in the Packages text box, make sure Dependencies is selected and click Install.
On a Debian system (e.g. Ubuntu) most required packages and programs can be installed directly through the official package manager system with the apt-get install command:
apt-get install r-base-core netcdf-bin libnetcdf-dev libxml2-dev \
libcurl3-dev seaview muscle pymol For Red Hat based systems (e.g. Fedora) the equivalent command is:
dnf install R-base R-devel netcdf-devel netcdf libxml2-devel \
libcurl-devel seaview pymol The Bio3D package can be 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)
Alternatively, Bio3D can be downloaded as source code e.g. from https://bitbucket.org/Grantlab/bio3d/downloads and installed with the command:
install.packages("bio3d_2.3-0.tar.gz")
Note that MUSCLE is not available from the Fedora package manager, but can be installed by:
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar xzvf muscle3.8.31_i86linux64.tar.gz
mv muscle3.8.31_i86linux64 /usr/local/bin/muscle
chmod a+x /usr/local/bin/muscleDSSP is also not available from a number of the package managers, but can be installed by:
wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp
chmod a+x /usr/local/bin/dsspA minimal version of Bio3D with reduced functionality (i.e. for reading/writing binary trajectory files, and fetching data from various databases) will require only the R base installed (i.e. no additional packages needed). Thus, only the R base will be required. In Ubuntu this can be obtained with the following two commands:
apt-get install r-base-coreinstall.packages("bio3d", dependencies=FALSE)
The Bio3D dependencies can be installed from within R with the command install.packages:
# install only the XML package install.packages("XML") # install all required install.packages(c("XML", "RCurl", "ncdf", "igraph", "bigmemory"), dependencies=TRUE)
To install the Bio3D package on Windows download the compiled binary .zip file from above.
Start R and from GUI click Packages \(\rightarrow\) Install Package(s) from local zip file then simply select your downloaded Bio3D zip file and click Open to finish the installation.
For the majority of users we recommend the use of the last stable release available from the main Bio3D website. 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.
There are a number of additional 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). A brief description of how to obtain these additional packages is given below.
Muscle is a fast multiple sequence alignment program available from the muscle home page http://www.drive5.com/muscle. The Bio3D functions seqaln() and pdbaln() currently calls the MUSCLE program, hence MUSCLE must be installed on your system and in the search path for executables if you wish to use this function.
A note for Mac and Unix users:
After downloading MUSCLE, it should be unzipped and renamed to just “muscle” and placed in a directory such as “/usr/local/bin/” (i.e. in your PATH).
STRIDE is another secondary structure analysis program available from the EMBL-Heidelberg. Stride is similar in functionality to the more prevalent DSSP (see above). However, stride is often much easier to setup on different computer systems as you may be able to simply copy or link to the stride executable distributed within every version of VMD (see below).
SEAVIEW is a graphical multiple sequence alignment editor. Download information and documentation are available from PBIL http://pbil.univ-lyon1.fr/software/seaview.html. I use Seaview to manually check and edit protein sequence alignment files prior to detailed analysis. I believe this should be done with every alignment regardless of how accurate the various automatic tools are supposed to be.
Clustal Omega is multiple sequence alignment program that can be used as an alternative to MUSCLE (needed e.g. for functions seqaln() and pdbaln()). Clustal Omega is available from http://www.clustal.org/omega/.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics. Visit the VMD website for download information and documentation http://www.ks.uiuc.edu/Research/vmd/.
PyMOL is another visualization program. Bio3D functions pymol.dccm() and pymol.modes() require PyMOL to be in your search path. PyMOL is available from http://www.pymol.org.
Ideally, as mentioned previouly, MUSCLE and DSSP should installed on your system and be in the search path for executables. To test this you should be able to call these programs from the command line with just their name from any directory.
For Mac and Linux you can find out whats in your PATH by launching your favorate Terminal program (on Mac one called Terminal can be found in Applications/Utilities folder) and entering:
echo $PATHAnd the result should be like this…
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/binSo this is stating that you can run Unix style applications located in 5 default locations of path in the file system:
/usr/bin
/bin
/usr/sbin
/sbin
/usr/local/binYou can add extra locations to your path by creating or editing an existing .bash_profile file in your home directory. This file should contain a line like the following:
export PATH="/my/new/path:$PATH" You can now put muscle and dssp in any of the locations listed by echo $PATH, including /my/new/path/, which of course you should change to something sensible for you.
For Windows, right click “My computer” -> click “Change settings” -> Advanced -> Environment Variables -> From “System variables” list find “Path” and click “Edit” -> Add the path to your programs at the end of the line.
If you have read this far, congratulations! We are ready to have some fun and move on to other package vignettes that describe various analysis including Molecular Dynamics Trajectory Analysis, Correlation Network Analysis (where we will build and dissect dynamic networks form different correlated motion data), enhanced methods for Normal Mode Analysis (where we will explore the dynamics of large protein families and superfamilies), and advanced Comparative Structure Analysis (where we will mine available experimental data and supplement it with simulation results to map the conformational dynamics and coupled motions of proteins). Happy Bio3Ding!
The version number of R and packages loaded for generating the vignette were:
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.25 crayon_1.3.4 rprojroot_1.3-2 assertthat_0.2.1
## [5] R6_2.4.1 backports_1.1.9 magrittr_1.5 evaluate_0.14
## [9] stringi_1.5.3 rlang_0.4.7 fs_1.5.0 ragg_0.3.1
## [13] rmarkdown_2.3 pkgdown_1.6.1.9000 desc_1.2.0 tools_4.0.2
## [17] stringr_1.4.0 yaml_2.2.1 xfun_0.17 compiler_4.0.2
## [21] systemfonts_0.3.1 cpp11_0.2.1 memoise_1.1.0 htmltools_0.5.0
## [25] knitr_1.29The latest version of the package, full documentation and further vignettes (including detailed installation instructions) can be obtained from the main Bio3D website: http://thegrantlab.org/bio3d/↩︎