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:

> cd /path/to/install/
> 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:

> denss.py -f 6lyz.out

However, to run DENSS and get publishable results, you must perform averaging of at least 20 individual reconstructions. To run averaging with DENSS, type:

> denss.all.py -f 6lyz.out

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:

> python -m pip install --user numpy scipy matplotlib

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:

> cd $HOME

Then, download (i.e. clone) the DENSS git repository from GitHub:

> git clone https://github.com/tdgrant1/denss.git

This will download the DENSS code and put it in a new directory named “denss”. Then move into the denss directory and install DENSS:

> cd denss
> python setup.py install

Once you have DENSS installed, running a single reconstruction is as simple as:

> denss.py -f 6lyz.out

However, to run DENSS and get publishable results, you must perform averaging of at least 20 individual reconstructions. To run averaging with DENSS, type:

> denss.all.py -f 6lyz.out

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:

> cd /path/to/denss/
> git pull
> python setup.py install