I'm using Molden, a molecular modeling program in the Xming X-Windows server, and when I set it up to put it's myriad subwindows into a single frame, I seem to lose the ability to move them around and bring them forward (on top of other windows).

In the below picture the "Directory..." window should be above the window with more buttons, as I'm trying to open a file.

enter image description here

How do I do this in Xming, or assuming this is like X-Windows anywhere, in X-Windows.

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Your X session isn't running a window manager of any kind. Ask the administrator of the remote system what window managers are available (icewm, fvwm, etc.). Then, if you're running molden from an xterm or similar prompt, you can run the window manager first, then run molden. Something like:

$ fvwm & # Run window manager in background
$ molden
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I'm actually running the program and X-windows server all locally – Nick T May 17 '11 at 19:57
You still need a window manager (don't know what you'd use on Windows), or to let it run in multiple windows (i.e., not all in one X frame). – Mike Renfro May 18 '11 at 2:10
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