Sunday 8 June 2008

Glucocorticoid receptor (2)

I played some more with the receptor from last week. Here are some more images. The trick is setting multi-layer transparency in pymol (Settings - Transparency - Multi-Layer). Rendering takes quite long then, but it looks nice.

You can take a better lock at the ligand inside the binding pocket.

Or you can make this picture which looks kind of cool, I think.

This one shows the opening in the outside surface.

Two commands to mention are:

Changing the transparency of an object ("cha"):
set transparency, .1, cha
I can never quite remember the syntax for that.

Pymol has a nice way of parallelizing the rendering. The downside is that this will stop the whole system. If you want to keep working while rendering in a multicore machine, you can change the maximum threads:
set max_threads, 1

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