This issue occurs in case your environment does not seem to support WebGL.
First read Using PDBj's web interface and check your browser's version. In case your browser does not support WebGL, please upgrade it to the latest version or use an alternative modern browser. Also make sure that your driver is new enough and has not been blacklisted by your browser.
In the case of Linux, if Molmil does not work with the default graphics driver (e.g. nouveau), please try to install an alternative graphics driver (e.g. NVIDIA).1
1) This issue has been reported on CentOS 6.7 + Firefox ESR 38.6.0 + nouveau driver