Macs in Chemistry

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Installing Molden


A couple of people have mentioned problems installing Molden, a package for displaying Molecular Density from the Ab Initio packages, so I thought I’d give a quick guide. Precompiled binaries for MacOSX on Intel machines are available via FTP. Open a Finder window and type command K (Apple K) or select “Go to Server..” from the “Go” menu. This should open the dialog shown below, now type in the FTP server address as shown.

Click “Connect” and you should see the window below.

Select the MacOSX folder, this contains several programs and different versions of Molden. molden4.7.macosX (standard Xwindows version) gmolden4.7.macosX (opengl version) ambfor (the auxiliary amber/gaff force field program) surf (auxiliary program to create solvent accessible protein surfaces). Drag molden4.7.macosX to the applications folder. You now need to change the downloaded file to executable. Open a Terminal window and type

chmod ugo+x /Applications/molden4.7.macosX

To run this version of Molden you need X-windows often called X11, X11 is available as an optional install on the Mac OS X install disks. Run the Installer, select the X11 option, and follow the instructions. There are more details here. The X11 installer is now available from the XQuartz project

To run Molden start up X11 and in the Terminal window type


Depending on how you bash profile is set up you may not need to give the full path to the application. You should now have molden running.

I also spotted this tip on MacResearch from FJM.

“Those binaries have names such as molden4.7.macosX, if you rename it to something without any extension or anything which could appear as an extension, say to molden47macosX the OS recognizes them as executable binaries and you can double click on them without using the terminal. X app starts automagically and you can just can start to use molden without any contact with the terminal..”

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