Saturday, August 1, 2009

Chemistry Graphics Hassle on Ubuntu

Lately I have been using Ubuntu Linux instead of Windows, and on the whole I think I prefer Ubuntu:
  • Ubuntu starts-up and shuts-down faster than Windows
  • Open Office is faster with Ubuntu (I never use MS Word even on Windows)
  • security is much less of a problem (although I do use a virus scan package with Ubuntu)
  • and the geek factor of using Linux probably appeals to me as well
One difficulty for me has been finding chemistry-specific software to take the place of the Windows programs I am used to using. That situation improved a little bit today.

Avogadro and Ghemical are two programs I have been playing around with for building and doing simple calculations on 3D molecular structures. They both have a window that displays the molecule in 3D, and up until today that has been a problem for me. Frequently the desktop would "bleed through" so I couldn't see the molecule being displayed. Depending on what I was doing it was either inconvenient or a major annoyance. It would be so much easier to do things in Windows. That would involve re-booting the computer and starting Windows - something I try to avoid doing these days.

It turns out the solution was pretty simple, but I'm still a newbie with Linux and it took me a while. If I turn off the fancy graphics for the desktop, the problem goes away. The first time this idea occurred to me I went into the Compiz control panel and didn't know where to even start - and I wanted to be able to turn everything back on again if that didn't work. Compiz has LOTS of settings, I tried a few things without making matters any better.

Instead, what I should have done was go to the System Preferences and select "None" on the Visual Effects tab. Problem solved! The Visual Effects aren't all that important to me, but it's nice that I can turn them on and off so easily.

Now I can spend some time playing around with Avogadro and Ghemical to figure out what they do.


Marcus D. Hanwell said...

Glad to hear it worked out for you. Unfortunately the fancy composited desktop effects on Linux do not interact well with OpenGL based applications. I do most of my development with it turned off. I would be interested to hear about issues you encounter as you use Avogadro.

If we can make Avogadro more useful in your teaching we would certainly be open to ideas. We have Python scripting support, as well as native C++ plugins - either allow for a lot of customization. Avogadro binaries are released for both Mac and Windows too, should make it easy for students to install it on their computers.

Steve W said...

Thanks for your help Marcus. I'm looking forward to trying all the options.

Quantum_Flux said...

Cool programs.