There are many different software tools available to visualize and sometimes to edit protein structure files, eg. in PDB format. I am using a Windows System (Windows 10). Thank you for any suggestion.
Depends on the task - for viewing and creating publication quality images, I like to use PyMOL.
See my presentations of
Presentation Introduction to PyMOL
(point-and click menu interface)Presentation Intermediate PyMOL
(scripting)Presentation Advanced PyMOL
(plug-ins and extensions, making movies)You can get the pre-compiled open source version for windows free from this site:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol
The PyMOL wiki contains a very comprehensive documentation of all commands: https://pymolwiki.org/index.php/Main_Page
To add interactive viewing capability to a webpage, JMOL (http://jmol.sourceforge.net) is my tool of choice.
For interactive homology modeling, Deep View (https://spdbv.vital-it.ch) and UCSF Chimera (https://www.cgl.ucsf.edu/chimera/)
are good choices.
To analyze the results of molecular dynamics simulations, VMD (https://www.ks.uiuc.edu/Research/vmd/) is the free tool to use, while in the context of Xray structure determination, Coot (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) is a good choice.
These tools are free - try them out and test which one fits your needs. If you just want to view and create figures, PyMOL probably is the best fit. You can do simple editing in PyMOL, such as isolating individual molecules from a larger complex, delete parts of a molecule, substitute individual amino acids. It you need to do more serious molecular editing, you should choose a tool capable of proper energy minimization.
There are also free viewers which serve as "appetizer" for larger, for pay applications, such as Yasara view (http://www.yasara.org/products.htm#view).
See the rcsb pdb website for a more complete list:
https://www.rcsb.org/pages/thirdparty/molecular_graphics
I prefer VMD , it is both easy and compatible with NAMD if you want to extend your work from just visualization to molecular dynamics simulations. You can analyze and visualize your structure easily. I have created a youtuble video list called " VMD tutorial for dummies" it explains everything from scratch.
https://www.youtube.com/playlist?list=PLhYF9QNr23IaG-aFub24_T8XnIbJb7fNU
you may also refer to the official pdf tutorial of the program (attached)
best regards
Depends on the task - for viewing and creating publication quality images, I like to use PyMOL.
See my presentations of
Presentation Introduction to PyMOL
(point-and click menu interface)Presentation Intermediate PyMOL
(scripting)Presentation Advanced PyMOL
(plug-ins and extensions, making movies)You can get the pre-compiled open source version for windows free from this site:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol
The PyMOL wiki contains a very comprehensive documentation of all commands: https://pymolwiki.org/index.php/Main_Page
To add interactive viewing capability to a webpage, JMOL (http://jmol.sourceforge.net) is my tool of choice.
For interactive homology modeling, Deep View (https://spdbv.vital-it.ch) and UCSF Chimera (https://www.cgl.ucsf.edu/chimera/)
are good choices.
To analyze the results of molecular dynamics simulations, VMD (https://www.ks.uiuc.edu/Research/vmd/) is the free tool to use, while in the context of Xray structure determination, Coot (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) is a good choice.
These tools are free - try them out and test which one fits your needs. If you just want to view and create figures, PyMOL probably is the best fit. You can do simple editing in PyMOL, such as isolating individual molecules from a larger complex, delete parts of a molecule, substitute individual amino acids. It you need to do more serious molecular editing, you should choose a tool capable of proper energy minimization.
There are also free viewers which serve as "appetizer" for larger, for pay applications, such as Yasara view (http://www.yasara.org/products.htm#view).
See the rcsb pdb website for a more complete list:
https://www.rcsb.org/pages/thirdparty/molecular_graphics
Deepview (https://spdbv.vital-it.ch/) is a free program that's nice for viewing pdb-files and for making publication-grade figures. However, further development seems to have stopped.
Has anybody tried such programs with the (relatively) cheap VR-goggles that have come onto the market for gaming?
Dear professor Engelbert Buxbaum , I tried VMD with both VR-goggles and sticks it was amazing experience.
Kindly have a look at the photo attached :)
It must be. DeepView can use the anaglyph (red/blue) technique, but that isn't quite the same.
See this page for stereo hardware supported by PyMOL:
https://pymolwiki.org/index.php/Stereo_3D_Display_Options
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