On Jun 7, 2012, at 8:15 AM, Bala subramanian wrote:

model=chimera.openModels.open('mypdb.pdb')
res=model[0].residues
grp = getPseudoBondGroup("mybonds", associateWith=[model])

Hi Bala,
The above lines need to be different.  They either need to be

model=chimera.openModels.open('mypdb.pdb')
res=model[0].residues
grp = getPseudoBondGroup("mybonds", associateWith=model)

or

model=chimera.openModels.open('mypdb.pdb')[0]
res=model.residues
grp = getPseudoBondGroup("mybonds", associateWith=[model])

I recommend the latter, since in that one 'model' is a single model, not a list of models.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu