[Chimera-users] Create oxime functional group

Eric Pettersen pett at cgl.ucsf.edu
Wed Oct 4 10:42:08 PDT 2017


Hi Jim,
	Chimera, perhaps unrealistically, prefers to make the central ring of the fused-ring system aromatic, and therefore puts a single bond between the ring and those nitrogens, which requires adding a hydrogen to each of them.  You can force Chimera to think otherwise by assigning a different atom type to those nitrogens with the following command (Favorites->Command Line):

setattr a idatmType N2 @n2,n3

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 4, 2017, at 9:25 AM, Wikel, Jim <jimwikel at iu.edu> wrote:
> 
> Hello,
> 
> I recently had difficulties with creating a particular structure in Chimera.  The SMILES is depicted below.  The problem is I have not been able to represent the oxime portion of the molecule.  I have tried to reset atomtypes, redrawing the structure, adding and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution.   Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization.  I am puzzled and suspect I may be doing fundamentally wrong.  Any advice would be helpful.
> 
> CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1​
> 
> Thanks you.
> jim
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