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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?

genpfault
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Shane
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  • Isn't the RasMol source code available? – PhiS Jul 25 '11 at 13:58
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    Why do you want to implement yet another visualizer? Is it a CG exercise? Or, what kind of feature(s) do you think is/are missing from currently available programs (PyMOL, Chimera, Jmol, ...)? Can you ask in the respective mailing lists for the missing features? – HongboZhu Apr 03 '12 at 11:50

3 Answers3

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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.

joaquin
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  • allow me to be constructve and point out that that is a complete solution that uses python to script the pymol application and nothing else. also, since he isn't enrolled in college, he would have to pay $20,000 or how much ever it costs to use pymol. – marinara Jul 22 '11 at 16:49
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    PyMOL is an open-source program. You can compile your own version from the source code and it does not cost money. Linux install: http://www.pymolwiki.org/index.php/Linux_Install Windows install is a bit tricky, but doable: http://www.pymolwiki.org/index.php/Windows_Install Its source code is available as python, or C/C++. You will really benefit from it if you want to start your own implementation. – HongboZhu Apr 03 '12 at 11:57
  • @HongboZhu Right, but in the case of windows, it is not difficult at all to start with pymol: as I already indicated, you can get (free) windows binary installers from Gohlke's repository. Seems marinara did not notice my edit and did not corrected/deleted his comment – joaquin Apr 05 '12 at 00:22
  • @joaquin, Gohlke's binary compilation is awesome. But notice that there are many restrictions (windows version, python version, CPU variation). I am sure for a lot fresh users it suffices. But there are cases when you bump your head against wall just because the binary does not work. – HongboZhu Apr 05 '12 at 07:48
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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

Jiahao Chen
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nathanael
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  • You can get the source from sourceforge (http://sourceforge.net/projects/pymol/files/pymol/1.4.1/). If you want binary installers you can get them from Golhke site as I indicated in my post – joaquin Jul 22 '11 at 17:42
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    There is still the free version of pymol. http://sourceforge.net/projects/pymol/ Pymol is totally capable of doing anything, it just might take some serious exploring/experimenting to figure out to make that happen. – Ryanmt Jul 22 '11 at 17:45
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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.

Ryanmt
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