Is there an (un)documented way of merging multiple molecular objects in Pymol into one molecule, which then can be written in a nicely formatted PDB file? I cobbled something cludgy together with ‘multisave’ and a couple read-sort-save cycles, but this is ugly and probably quite fragile. An API function might be much more robust. Is there a provision like this in ChemPy? I’ve already taken care of adjusting each molecule to be unique with respect to chain IDs and IDs, so that would not be an issue.
Any pointers would be appreciated.