[Chimera-users] Create oxime functional group

Wikel, Jim jimwikel at iu.edu
Wed Oct 4 19:53:03 PDT 2017

?Hi Eric,

Thanks for this approach.  I found it worked nicely too.  I had tried to change the atom type via the user interface but I could not get one that didn't add the extra hydrogen.


From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Wednesday, October 4, 2017 1:42 PM
To: Wikel, Jim
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Create oxime functional group

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 Pettersen
UCSF Computer Graphics Lab

On Oct 4, 2017, at 9:25 AM, Wikel, Jim <jimwikel at iu.edu<mailto:jimwikel at iu.edu>> wrote:


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.


Thanks you.
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