?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. jim ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, October 4, 2017 1:42 PM To: Wikel, Jim Cc: chimera-users@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 Eric Pettersen UCSF Computer Graphics Lab On Oct 4, 2017, at 9:25 AM, Wikel, Jim <jimwikel@iu.edu<mailto:jimwikel@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Thank you Eric and Elaine for the prompt responses. They were helpful and I am proceeding with my project. I had entered the structure without going through the smi23d web service. I had assumed the web service was gated by the IU network and I am working on this off site. I failed to even try it. Thanks. jim ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, October 4, 2017 1:54 PM To: Wikel, Jim Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Create oxime functional group Hi Jim, If you’re processing the molecule on its own (e.g. not trying to minimize it in a binding site), the short answer is to not minimize it in Chimera. If you got it via the smi23d web service from Indiana University, e.g. Chimera command open smiles: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 … then the molecule has already been through geometry optimization with MMFF94. The Chimera Reply Log reports whether the Indiana U web service was used (and when I tried the SMILES string above, it was). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html#fetch> (MMFF94 is mentioned in the paper linked to the smiles fetch description) In Chimera, if you minimize that fetch result without adding further hydrogens or changing atom types, the result seems bad (large deviation from planarity). If you change the atom types to N2 as Eric said, I expect it to be better-behaved. Nevertheless, I would not minimize it at all unless analyzing it within some larger system. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 4, 2017, at 9:25 AM, Wikel, Jim <jimwikel@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users