[Chimera-users] adding pseudo bonds

[Eric Pettersen]

On May 12, 2009, at 8:39 AM, Elaine Meng wrote:

> Hi JD,
> The "user interface" (i.e. no programming) way is to create a text
> file listing the desired pseudobonds and their colors and read it in
> with PseudoBond Reader.  The tool and file format are described here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html
>>
>
> I don't know the python way, but perhaps looking in the code for
> PseudoBond Reader will help ( share/PBReader/ within your Chimera
> installation).

The "programming way" is ('metal' and 'chel' are the two atoms):

mol = metal.molecule
from chimera.misc import getPseudoBondGroup
group = getPseudoBondGroup("coordination complexes of %s (%s)" %  
(mol.name, mol), associateWith=[mol])
group.newPseudoBond(metal, chel)

--Eric