Hi...
I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera?

Absolutely.  That's the purpose of psuedobonds, to show non-covalent interactions between models such as hydrogen bonds, NMR constraints, hydrophobic interactions, etc.

First I should mention that you don't necessarily need to use Python to do this.  The PseudoBond Reader tool can create pseudobonds between models.  But if you are writing a Python script anyway, you would first create a PseudoBondGroup to contain your pseudobonds like so:

from chimera.misc import getPseudoBondGroup

grp = getPseudoBondGroup("my pseudobonds")

and the create a pseudobond between atoms a1 and a2 with:

pb = grp.newPseudoBond(a1, a2)

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu