I am trying to create an image of my molecule of interest fused to Yellow Fluorescent Protein. I have the PDBs for both molecules loaded in Pymol and I just wish to ligate the amino terminus of YFP to the carboxy terminus of the other PDB.
I have tried the create bond command (pk1)-(pk2) [Ctrl-T]
but I get the error message "Selector-Error: Invalid Selection Name."
Do I need to somehow save the two molecules as 1 PBD file then try creating the bond?
I had a similar problem using SPDV deep view.
If anyone knows how to do this in either platform I'd be grateful.