Pymol movie - ligand and receptor binding.

Question

[Hansen_869]

HI!

I'm trying to figure out how to make a movie in pymol, where a ligand binds with its receptor. Ligand and receptor are in two separate PDB files. I know where the ligand binds to the receptor, I just need an animation where the ligand slowly approaches the receptor binding site, connects, and after a few seconds, goes back to its initial position (unbinded). I have been trying to look for tutorials, but I've failed to find one similar to this.

Hope you can help, thanks!

Answer 1

[Mensur Dlakic]

Start with the bound complex, translate the ligand out by say 30 angstroms, then bring it back by translating in reverse one angstrom at a time. Those commands are easy to script in PyMol. The toughest part will be finding the complex orientation so you can do the translation along a single axis.

[Hansen_869]

Thanks a lot! I'll give it a try!