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DNA Geometry with cadnano

cadnano

This article introduces a tool you can use to work on three-dimensional DNA origami. The package is called cadnano, and it's currently
being developed at the Wyss Institute. With this package, you'll be
able to construct and manipulate the three-dimensional representations
of DNA structures, as well as generate publication-quality graphics of
your work.

Because this software is research-based, you won't likely find
it in the package repository for your favourite distribution, in which
case
you'll need to install it from the GitHub
repository.

Since cadnano is a Python
program, written to use the Qt framework, you'll need to install
some packages first. For example, in Debian-based distributions, you'll
want to run the following commands:


sudo apt-get install python3 python3-pip

I found that installation was a bit tricky, so I created a virtual Python
environment to manage module installations.

Once you're in your activated
virtualenv, install the required Python modules with the
command:


pip3 install pythreejs termcolor pytz pandas pyqt5 sip

After those dependencies are installed, grab the source code with
the command:


git clone https://github.com/cadnano/cadnano2.5.git

This will grab the Qt5 version. The Qt4 version is in the repository
https://github.com/cadnano/cadnano2.git.

Changing directory into the
source directory, you can build and install cadnano with:


python setup.py install

Now your cadnano should be available within the virtualenv.

You can start cadnano simply by executing the cadnano
command from
a terminal window. You'll see an essentially blank
workspace, made up of several empty view panes and an empty inspector
pane on the far right-hand side.

Figure 1. When you first start cadnano, you get a completely
blank work space.

In order to walk through a few of
the functions available in cadnano, let's create
a six-strand nanotube. The first step is to create a background that
you can use to build upon. At the top of the main window, you'll find
three buttons in the toolbar that will let you create a „Freeform“,
„Honeycomb“ or „Square“ framework. For this example,
click the honeycomb button.

Figure 2. Start your construction with one of the
available geometric frameworks.



Source

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Veröffentlicht von Paul Christoph

Mein Name ist Paul Christoph Feichtinger, geboren am 15.5.1991 in Oberndorf bei Salzburg und mittlerweile stolzer Autor von 11 Büchern (7 in Deutsch und 4 in Englisch), 4 Apps (bald kommt Nummer 5) und dieser Webseite. Bei Paul Solutions bekommen alle Bücher und Apps ihre Form. Sieh dich ruhig ein bisschen auf meiner Webseite um, vielleicht gibt es auch für dich noch das ein oder andere zu entdecken. ;-)

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