> Now I want to have my structures in an orthographic view (for top/side view). 
> I tried to edit glwidget.cpp from the stable release as below.
> It now seems to display stuff orthographically but it looks like depth 
> queuing doesn't work anymore. Bond sticks are above their atoms and atoms in 
> the back are above atoms in the front. (see attached picture).

It's not as simple as just that. The camera class would need changes at the 
very least -- there may also be some further code in other places too (look for 
gluPerspective calls).

For example, here's a description of the reverse process I found using Google 
for you:
http://www.opengl.org/discussion_boards/ubbthreads.php?ubb=showflat&Number=274350

Some other possibly useful links:
http://www.songho.ca/opengl/gl_transform.html
http://www.opengl.org/discussion_boards/ubbthreads.php?ubb=showflat&Number=208892
http://stackoverflow.com/questions/5765309/converting-orthogonal-camera-to-perspective-opengl

It's certainly possible to add an orthographic view, but it will require some 
time to get familiar with OpenGL transformations. As I haven't touched that 
code in ages, I'm not the best person to ask.

Hope that helps,
-Geoff
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