Installation Instructions
Below you’ll find all the necessary information for downloading and installing DENSS. For detailed instructions on how to use DENSS, visit the Tutorial page.
Quick Start
If you have the required dependencies installed (i.e. Python 2.7/3.6/3.7/3.8, NumPy, SciPy, and optionally Matplotlib), then you may proceed to download and install DENSS with a few commands:
$ git clone https://github.com/tdgrant1/denss.git
$ cd denss
$ python setup.py install
Then to run a single electron density reconstruction with DENSS using default parameters, simply type:
However, to run DENSS and get publishable results, you must perform averaging of at least 20 individual reconstructions. To run averaging with DENSS, type:
For more details about averaging, see the Tutorial pages.
Requirements
To run DENSS, you must have some dependencies installed. These include Python (tested with versions 2.7, 3.6, 3.7, and 3.8), NumPy (v1.10+) and SciPy (and optionally Matplotlib (v2.3+)). One great way to get all these packages easily on most platforms is using a package manager such as Anaconda or Enthought. The current version of DENSS was built and tested using Anaconda.
Alternatively, NumPy, SciPy and Matplotlib are very common packages and are available through the Python Package index and can be installed using the simple command:
If you’re having difficulty installing these dependencies, these and other useful tips for installing these packages can be found on the SciPy website.
Clone DENSS
To download DENSS from GitHub, open a terminal window. Go to the folder you where would like to install DENSS (e.g. your home directory) by typing at the command prompt:
Then, download (i.e. clone) the DENSS git repository from GitHub:
This will download the DENSS code and put it in a new directory named “denss”. Then move into the denss directory and install DENSS:
$ python setup.py install
Once you have DENSS installed, running a single reconstruction is as simple as:
However, to run DENSS and get publishable results, you must perform averaging of at least 20 individual reconstructions. To run averaging with DENSS, type:
To run DENSS with more advanced options, see the Tutorial page.
Update DENSS
DENSS is updated quite frequently. If you have already installed DENSS and simply want to update to the latest version, type:
$ git pull
$ python setup.py install
EMAN2
One can optionally install EMAN2 (see below for summary of install instructions) to perform averaging. A bash script called superdenss is provided for conveniently running the entire pipeline in parallel on a multicore processor (assuming GNU parallel is also installed, otherwise DENSS runs in a loop). To run superdenss with default parameters, type:
To run the EMAN2 averaging procedure you must also have EMAN2 installed. Also recommended for installation is GNU parallel, which runs multiple reconstructions with DENSS in parallel on a multicore machine. EMAN2 is straight forward to install using the binaries they provide (scroll down the page a bit until you see the EMAN2.xx links, download the latest version, note where it was downloaded, e.g. your Downloads folder). Choose a folder where you like to install software (such as your home directory). For most users, installing EMAN2 will simply consist of the following commands:
$ mv $HOME/Downloads/eman2.21.MacOS.sh .
$ bash eman2.21.MacOS.sh
But, obviously, use the correct filenames and paths for your platform. If you have issues getting EMAN2 installed, see their installation page.