[Chimera-users] Paint a pseudobond....

Eric Pettersen pett at cgl.ucsf.edu
Thu Jun 24 12:58:48 PDT 2010

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 Pettersen
                         UCSF Computer Graphics Lab

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