You know those super pretty “pictures” of proteins that you see in journals and stuff? A lot of them were made using a free software called PyMol – although many of the cryo-EM ones were likely made in ChimeraX. Today I want to introduce you to PyMol and show you how you can use it to view the atomic structures of proteins, play around with them in 3D, view them in different representations, and export pretty pictures. It’s definitely not a real tutorial – I’m by no means an expert! I just use it to do what I need when I need. So today I want to just get people introduced and help familiarize them to the point they feel they can play around and not just feel lost!
note: apologies for the weird video angles
correction, sorry: you actually can show the surface for selections (not just objects) but if you want to alter transparency, that (and other functions) is an object-level function so you’ll want to extract your selection to an object
I would say that I half-know how to use it… But the great thing is that there’s a really great PyMol Wiki. If you Google a PyMol question, it’ll probably direct you there and you’ll hopefully find your answer (if not there’s always Twitter, where people can usually help you). The Wiki also has tutorials and you can find it here: https://pymolwiki.org/index.php/Main_Page
If you’re looking for good video tutorials, here’s a good place to start – “Molecular Visualization Using PyMOL” by Bevan & Brown Lab https://youtu.be/aDmOe1ZgTz0
To download the “incentive” version of PyMol (where you need a license in order to export nice figures but can still basically run it without a license) https://pymol.org/2/
You can get a FREE license if you’re a student or teacher. And many research labs have academic licenses – so check with your peeps! Here’s the link to the various options https://pymol.org/2/buy.html?q=buy
And ANYONE can download the open-source version which lacks some of the advanced functionality, but can do the rest.
Here’s a comparison: https://pymol.org/compare.html
And here’s a link to download: https://github.com/schrodinger/pymol-open-source
Here’s the link for downloading ChimeraX, free: https://www.rbvi.ucsf.edu/chimerax/
A third option is CCP4 Molecular Graphics, which I haven’t used as much but you can download it free here: https://www.ccp4.ac.uk/MG/
more on Ago & RNAi: https://bit.ly/awesomeAgo
more on the PDB: https://bit.ly/pdbstructures