[Chimera-users] How to append functional groups to a residue

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 1 17:36:53 PDT 2005

	The short answer is that you can't, but we want to add that ability 
(need to prioritize it with other requests).  The slightly longer 
answer is that if you know Python, it's not too hard.  in 
chimera/molEdit.py there is an addDihedralAtom() routine that allows 
you to add atoms given their chemical element along with distance, 
angle, and dihedral from other atoms (or from spatial positions).  In 
that same file there is also an addBond() routine which allows you to 
add bonds.
	If there are only one or two functional groups you actually want to 
add, I could send you some code that would add them if you tell me 
which ones you need.  If you really need a wide spectrum of groups, 
then I guess the short answer applies.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Jun 27, 2005, at 3:24 PM, C. Parry wrote:

> Hi Chimera Peoples -
> My question is how does one append a functional group
> (say, nitro, bromine, ..., or metal) to a residue
> (say, tyrosine, ..., adenine). This would involve
> replacing some atom or group. I am aware of 'swapa,'
> 'swapna' commands but these are straight forward
> one-for-one changes of whole residues.
> Thanks.
> C. Parry
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