Running on your Desktop

Jolecule is also designed to run on your desktop, independent of this website. First you need to download the Jolecule package from Github.com:

   jolecule-master.zip

You then need to install Node.js, the Javascript eco-system. Once Node.js is installed, go to the Jolecule directory, and install the modules required:

> npm install

This will include the installation of the Electron package, which enables Desktop mode for Jolecule.

Desktop Electron mode of Jolecule

On the Linux/MacOSx command-line, run from the Jolecule directory:

> ./jol-electron.sh [PDB file] | [directory]

This will run the desktop version of Jolecule that allows you to directly read the PDB files on your drive. As well, there is a useful left-hand panel that will list all PDB structures in the current directory, with the TITLE field from the PDB files.

You can easily switch files by clicking on the different PDB entries on the left.

For any PDB file, say 1be9.pdb, any views saved will be written to the file 1be9.views.json . These views will be automatically reloaded if the PDB file is later reloaded.

Creating a self-contained Webapp

Once you've created a bunch of views for a PDB structure. You can create a static webapp for the PDB structure and its views. These webapps are self-contained - they can be viewed simply by opening them in a browser. They can be opened locally, remotely on a website, or sent to others.

To create a Jolecule webapp, on the command-line on Linux/MacOSX, in the Jolecule directory, which contains your PDB file, say 1be9.pdb, and the views file, say 1be9.views.json, run:

> ./jol-static.js 1be9

This will create a folder 1be9-jol with the webapp, which can be opened in your browser by opening the following file:

> open 1be9-jol/index.html

There are different ways to setup the webapp, for instance, you can animate a slideshow, or rotate the protein in a given view. To choose the mode, you can edit the parameters of the Jolecule widget in 1be9-/jolindex.html

The parameters are described in the embedded widget guide.