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bioinformaticspymol

How to bind a ligand to a protein in PyMOL?

I currently have a protein which is the focus of my study (.pse file) and several ligands (.pdb files) that I wish to bind to this protein to view where and how they bind. However, there are no biological sequences for the given molecules, so I am wondering what command I need to bind the ligand molecules to the main protein 1 at a time.

When I open the ligand files from the main protein file, I can see the ligand molecules but does this show an accurate representation of where they are actually binding?

Thank you!

Solution

  • For those of you who are wondering, you simply need to open your protein file (from MOE) within PyMOL and it will bind correctly, as binding information is stored in the file from MOE.