[Chimera-users] Selection through bond and fragment naming

[Eric Pettersen]

On Mar 14, 2011, at 1:44 PM, Jean Didier Pie Marechal wrote:

> Dear all,
>
> thanks a lot for your answers. I seem to have a problem though.
> When running the script, one way or another I always ends up with  
> something like:
>   a.residue.removeAtom(a)
> AttributeError: 'NoneType' object has no attribute 'removeAtom'
> AttributeError: 'NoneType' object has no attribute 'removeAtom'
>
>  File "M:\REUNIONS\dibuixos\Manipulate_structure\newres.py", line  
> 20, in <module>
>    a.residue.removeAtom(a)

So, it seems like the script I sent was mildly buggy.  In particular,  
"a.residue" gets used even after the atom has been removed from the  
residue.  So, you need to change this:

>> # withdraw atoms from their current residues
>> for a in atoms:
>> 	a.residue.removeAtom(a)
>> 	if len(a.residue.atoms) == 0:
>>       	a.molecule.deleteResidue(a.residue)

to:

# withdraw atoms from their current residues
for a in atoms:
	res = a.residue
	res.removeAtom(a)
	if len(res.atoms) == 0:
       	a.molecule.deleteResidue(res)


Sorry about that!

--Eric