This page is based on the ChemDoodle 2D instructions, which are identical, except for the download. Make sure to download ChemDoodle 3D from here. Then follow the instructions below replacing the ChemDoodle file names with the ChemDoodle 3D file names.
After downloading ChemDoodle, use Terminal to run the BIN and install ChemDoodle. Then open the installed ChemDoodle directory and run the ChemDoodle shell script. If you encounter any issues, please consult the Troubleshooting Common Installation Issues section.
- Download ChemDoodle for Linux from the following link if you haven’t already done so. ChemDoodle is supported on any Linux distribution with the official Oracle Java installed. We recommend and test Linux Mint. We also test on OpenSUSE, Debian and Fedora Linux. ChemDoodle does NOT support OpenJDK, IcedTea, GNU Java, or any other non-Oracle version of Java. With unsupported Java distributions, ChemDoodle will run slowly, have broken functions and may not even run at all.
Download ChemDoodle 3D v3.0.0 for Linux
- ChemDoodle3D-linux-3.0.0.bin, a Linux bin, will be downloaded to your computer. You may check the MD5 checksum with the following number to verify your download.
MD5 checksum: cac7520c8287f20738fddb38ca009fce
- Open Terminal and change the directory (using the cd command) to the directory you downloaded ChemDoodle to. Browsers will usually download files to the ~/Downloads folder if you didn’t explicitly set the download path. You can check the contents of a folder using the ls command.
- After locating the BIN, use the following command to run it. ChemDoodle will be installed in your present working directory; you can move the BIN to a different location to change where ChemDoodle will be installed. Or feel free to move the installation folder after the installation completes.
- If you are satisfied with the installation location and are reminded about using the official Oracle Java distribution, press the return key to install ChemDoodle.
- Now open the newly installed ChemDoodle folder to see what was installed. The install automatically registers the ChemDoodle application with GNOME environments, so you should see ChemDoodle entries in the Linux application menus.
To place a Launcher for ChemDoodle in your system tray, just drag the ChemDoodle application menu item from the Linux application menu onto the system tray.
- Double-click on the ChemDoodle shell script or click on the shortcut in the system tray to run ChemDoodle. Do NOT use the Java JAR, ChemDoodle.jar, to run ChemDoodle.
The first time you open ChemDoodle, you will be greeted with our software license. Please read and understand it, and then choose to accept it. If ChemDoodle does not start or you see an error, please consult the Troubleshooting Common Installation Issues section.
Type or copy and paste the activation code we provided to you when you purchased ChemDoodle, and then click the Verify button.
- ChemDoodle will build and a confirmation screen and user’s guide will follow. Congratulations, ChemDoodle is now activated and ready to use at any time!
- To uninstall ChemDoodle, simply drag the entire ChemDoodle folder to the Trash.
- Java is not installed. If you see a message similar to the one in the following image, then ChemDoodle cannot find Java. Either make sure your classpath is correct and contains Java or go to www.java.com to quickly and easily install Java for free.
- A non-official Java distribution is being used. If you see a popup message similar to the one in the following image, then ChemDoodle is running with a non-official version of Java. ChemDoodle does NOT support OpenJDK, IcedTea, GNU Java, or any other non-Oracle version of Java. With unsupported Java distributions, ChemDoodle will run slowly, have broken functions and may not even run at all. Either make sure your classpath is correct and contains the official Oracle Java distribution or go to www.java.com to quickly and easily install the official Oracle Java for free.
Detailed Instructions – For those inexperienced with Linux
Troubleshooting Common Installation Issues
If ChemDoodle does not start or you see an error popup, then open terminal, change the present working directory to the ChemDoodle installation folder, and run the shell script using the following command to catch any diagnostic errors. Then check for solutions below. If you encounter an error not addressed below, please copy and paste all text from Terminal and send it to us.