[Chimera-users] Error when making Covalent bonds

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 25 10:48:38 PDT 2005

Hi David,
	Chimera's definition of molecule models is that there are no covalent 
bonds between them, which is why you get the error message.  I've 
created a short Python script (attached) which will take any selected 
molecule models and create a new model consisting of the union of the 
selected models.  You will be able to make your bond in this new model. 
  The script doesn't try to do anything smart about reconciling residue 
names/numbers or chain IDs.  You might have to edit one of the source 
files for your models beforehand if this is problematic.  You can run 
the script with "open dupMol.py" in the command line or by using 
"File...Open" with file type set to Python or one of the "all" types.
	The new model will completely overlap with the selected models, so you 
will have to hide/close/move the selected models to easily work with 
the new model.


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

On Oct 25, 2005, at 12:31 AM, David Chenoweth wrote:

> Hi!
> I am trying to pull up two molecules in chimera and link them by
> forming a covalent bond between a N and C atom.  I am selecting only
> the N of one molecule and the C of the other.  When I go to command
> line and use the bond sel command I get the following error message.
> Type error: Cannot form covalent bond joining two molecules.
> Does anyone know how to get around this.
> Thanks,
> David C.

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