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.

ok so I know this is an answer to my own question but it is also an FYI for anyone else who uses Pymol

This is a useful link for all the commands in Pymol
http://www.pymolwiki.org/index.php/Category:Commands

For my own problem the answer was the command fuse (pk1),(pk2) where pk1 and pk2 are the atoms on each molecule between which you wish to form the bond.

The create bond command is only good within the same molecule