First off, thanks for providing a free molecular dynamics service! It works great, except that I am unable to visualize my proteins in Jmol with Java applets due to the removal of NPAPI plugins in Firefox (I believe it’s also been dropped in Chrome and Safari). I resorted to running Java 6 in a legacy version of Firefox on a Windows XP virtual machine, but it’s inconvenient and slow. Have you considered upgrading to a JavaScript-based molecular graphics viewer? Thanks!
Hi Paul,
we have a version of MDWeb with added functionalities, one of them being jsmol to avoid the problems you mention. However, it was never functionally tested as MDWeb was, that’s why it was never publicly published as a new stable version. Anyway, if you want to give it a try, this is the URL:
http://mmb.irbbarcelona.org/MDWeb2/
In BioExcel we are trying to update this idea of free MD services (at least setup + configuration files) through GUIs such as web servers. Stay tuned with BioExcel web page or subscribe to our mailing list to hear about the news!
Thanks for using our tools!
-Adam-
Java applet requires a virtual run time error free backend like the one did at https://netgears.support/netgear-genie-support where the functionalities are chosen one by one.