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.h...
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