ProteinShop is a visualization tool for molecular structure. It is no longer maintained, but the source is made available under a GPL license.
This project offers an easy way to run ProteinShop on a local virtual machine for the purposes of evaluation, curiosity, and so forth. The tools used are Vagrant, Virtualbox, Chef, and Librarian-chef.
- Vagrant is a tool for managing Virtualbox virtual machines.
- Virtualbox runs virtual machines.
- Chef is a provisioning tool for setting software on a machine.
- Librarian-chef is a package manager for Chef cookbooks.
The virtual machine that can be set up here is a CentOS 6.4 64 bit OS.
- Setting up an alternative Ubuntu 12.04 VM.
- The AMBER energy calculator referenced in protein-shop/lib/input/README is as yet unexplored.
- Allowing ProteinShop to specify a path to its configuration file would be nice.
- Other tidying up of execution behavior, such as directing or configuring output, would also be good.
- Other tidying up of the ProteinShop folders to strip out possible build and test files.
- Any sort of extensive testing has yet to happen.
Changes have been made to the ProteinShop Makefile.
- Switch to using gfortran rather than g77.
Everything under /protein-shop is GPL, everything else here is MIT.
- Install the latest versions of Vagrant, Virtualbox, and Chef, and Librarian-chef.
- Checkout this project.
Then on the command line in this project directory, execute the following commands to install all the needed Chef cookbooks and fire up the CentOS virtual machine:
librarian-chef install
vagrant up centos-6.4-x86_64
Vagrant will download a base virtual machine image the first time you do this, then launch it and run a setup and provisioning process. The download and provisioning only has to be done once (unless you destroy the VM and start over, and even then Vagrant keeps a copy of the original downloaded base box).
Once launched you can log in to the machine with user vagrant and password
vagrant. Running this command in the project directory will also log you in
as user vagrant over SSH:
vagrant ssh centos-6.4-x86_64
This user has full sudo rights, so you can upgrade to root access from the
command line with sudo su as usual.
Using Vagrant to manage a VM that has a GUI is less reliable than using a headless VM. You will see the occasional failures wherein Vagrant fails to establish a connection to the server or fails to detect when the boot process completes.
Similar, the provisioning process requires downloading software from the internet, and that also sometimes fails.
If either of these things happens, then you will see red error messages from Vagrant. The best thing to do at that point is to force halt the VM and then retry, rerunning the provisioning if it hasn't yet completed:
vagrant halt -f centos-6.4-x86_64
vagrant up --provision centos-6.4-x86_64
For CentOS 6.4:
sudo yum install gcc-gfortran freeglut-devel fltk-devel fltk-fluid
You will have to add the remi and epel repositories to get access to many of the dependencies.
For Ubuntu 12.04:
sudo apt-get install gfortran binutils-gold freeglut3-dev libfltk1.3-dev fluid
Unfortunately this Ubuntu build appears to have issues; it compiles correctly, but fails to run. More investigation is needed.
After you are set up and the VM is running, you will find this project directory
shared with the VM under /vagrant. So the ProteinShop installation will be
under /vagrant/protein-shop.
To build the ProteinShop executable log in to the VM as user vagrant with
password vagrant. Then on the command line:
cd /vagrant/protein-shop/src
make clean
make
The ProteinShop source is a mix of C and Fortran 77 code. The original Fortran compiler used was g77, but getting this installed on modern *NIX machines is a real pain, so it has been replaced by gfortran.
To get ProteinShop running with sample protein data for Ubiquitin, you must
log in to the VM GUI as the vagrant user, open a command prompt, and run
these commands:
cd /vagrant/protein-shop/bin
./ProteinShop ../data/1UBQ.pdb
Note that you have to run the ProteinShop executable in the same directory as
the ProteinShop.cfg configuration file, which is located at
/vagrant/protein-shop/bin/ProteinShop.cfg.
You will need later versions than are probably available in the package respositories for your OS as of late 2013. Go to the source to get the latest stable builds and installers:
At minimum you will need Vagrant 1.3.4, Chef 11.6.0, and Virtualbox 4.2.*.
-
Run the following to obtain those packages that are usefully recent.
sudo apt-get install chef ruby1.9.1-dev sudo gem install librarian-chef
-
Download the latest Vagrant .deb package file. Don't use the older Vagrant version in the Ubuntu repositories.
-
Instructions for installing Virtualbox can be found at the Virtualbox site. For example, for to install a suitably recent version of Virtualbox, add this line to /etc/apt/sources.list:
deb http://download.virtualbox.org/virtualbox/debian raring contrib
Then run:
wget -q http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc -O- | sudo apt-key add -
sudo apt-get update
sudo apt-get install virtualbox-4.2