Hi Yasser, On Jun 24, 2010, at 8:41 AM, Yasser Almeida Hernández wrote:

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.

If it does, how would be the Python API code?

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