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How to launch the Download Tool using Java Web Start

The Download Tool launches a stand-alone application using the Java Web Start protocol. To view software requirements or if you have problems launching the application, please view the the Java Web Start troubleshooting guide.

The Download Tool can download multiples instances of PDB data files, individual sequence data files, and individual ligand data files. After entering the IDs of the files to download, select the button and a file called download_rcsb.jnlp will be downloaded and saved on your computer. Choose the option "Open with Java Web Start (default)" and check the box "Do this automatically for files like this from now on". Then click OK.

Launching Java Web Start

You will see the following dialogue if security settings are already correctly configured on your machine. Click Open to run the application.

Open JNLP file

Click Run on the RCSB Download Application window. It will guide the download process.

RCSB Download Application file chooser

Select where the file(s) should be downloaded and then click Choose.

RCSB Download Application

Click the Start Download button.

RCSB Download Application

A progress bar will displays 100% complete once all files are downloaded. Click Done to end the process.

RCSB Download Application


Based on the security settings on your machine, the following dialogue may appear. Please change the settings accordingly. The next images are a step-by-step guide on changing Security & Privacy settings and launching the Download Tool for Mac.

Can not launch JNLP due to security settings

Step 1: By default, Mac only allows apps downloaded from Mac App Store. Click the lock icon at the bottom of left-hand-side corn. You need to enter the password to make changes.

Change security settings

Step 2: Choose the option "Anywhere" under "Allow apps downloaded from". Then click the button Allow From Anywhere to confirm the change. You may also want to click the lock icon again to prevent further changes.

Open JNLP file

Step 3: Locate download_rcsb.jnlp and double click it to launch the application. When you launch the RCSB Download Application for the first time, you will see the following message. Click Open to run the download application.

RCSB Download Application