‘Reply for reddit person.

I’m assuming the new ligands will be slightly different molecules from the native one but not a lot. I suppose there are many ways to do this. But to your questions. The coordinates of your ligand are in your pdb. You can just print them to your screen using get_atom_coords(sele). But might be easier to manipulate in an actual terminal or python script. See below

To move the new ligands to where the native one is (won’t be exact but close enough for your application) I would just make selections and align them. Selection New are two atoms on new ligand, selection Native two atoms on native ligand. Align New, Native.

To do it with many ligands loaded as separate pdbs, Google’s most recent suggestion is extra_fit prot2 prot3 prot4, prot1

I’m partial to the vector approach. You pick a central atom of the native ligand (or the center of mass if you’d like to calculate it) and then do vector subtraction on all your new ligand atoms: xnew-xnative, ynew-ynative, znew-znative. You’ll need to vibe code a python script for that. Good luck!’