How to make PyMOL draw bonds between atoms in console / script?

I want a PyMOL script to automatically draw bonds for a given structure, e.g. between all palladium atoms, or between all palladium and sulfur atoms.

I can do this manually by the bond command, but need to know the identifiers of the atoms:

bond id 3, id 4
bond id 2, id 6
...

• How can I create all the desired bonds at once?
• It would also be helpful, if a bond is created only, if the distance between the atoms is within a specific cutoff radius.

After crawling the PyMol mailinglist, I managed to connect all atoms. e.g.

bond (elem pd), (elem pd)

draws bonds between all the Pd atoms.

---

Now to the cuttoff radius:

bond (elem pd), (elem s) within 2.5 of (elem pd)

draws bonds between all Pd atoms and all S atoms within the range of 2.5 of any Pd atom. This is resulting in a weired structure with very long bonds.

I think it's necessary to iterate over one of both selections to yield bonds within the desired cutoff radius only.

Instead, I make use of the find_pairs function of pymol (this is API only and thus has to be used in a python script).

from pymol import cmd, stored

pd_s_bonds = cmd.find_pairs('n. pd', 'n. s', cutoff=2.5)
for pair in pd_s_bonds:
    cmd.bond('index %s' % pair[0][6], 'index %s' % pair[1][7])