Protein structure visualization

Question

I've been asked to work on Protein structure visualization, something like RasMol where a user will be opening a pdb file to get the protein structure.

How I can generate protein structure from the pdb file?

I would like to code in Python and to visualize the structure should I be using OpenGL or VTK? are there any other modules that might help me in this regard?

Answer 1

You should try pymol that has a python interface.

Here you have a beginners tutorial of how to script pymol to interact with the views

As a student you can get pymol with no charge from the pymols site. In addition, Gohlke provides installers for 32 and 64-bit windows and python 2.6-2.7.

Answer 2

I think Pymol is not free anymore since it has to be purchased from Schrödinger. Couple of free programs: - JMol (bad!! don't use that except if you have no other choices) - PyMol (if you are academic) - Yasara - Discovery studio (Accelrys) - RasMol (No longer maintained) - VMD (the best program for visualizing trajectories). Very powerful but I never used it.

I don't know if you can do scripting in all of them.

I work a lot with PyMol and I did some plug in. The only limit is that you can use it as a viewer but nothing else. For example, you can not get an information by clicking on an atom.

good luck

Answer 3

Chimera http://www.cgl.ucsf.edu/chimera/ is another viewer. I think its license is more flexible than the pymol one.

You are writing your own? I think most of these answers are pointing you to implemented viewers. Good luck though, I imagine it will take a lot of work.