[Chimera-users] Chimera add H to NAD

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 3 13:46:02 PDT 2020

Hi Peter,
Chimera uses the bond lengths and angles to guess atom types.  It does not use (or even have a concept of) bond orders, so editing the bond orders in the mol2 file is not going to do anything.

First open the structure, label by atom type (e.g. menu: Actions.. Label...IDATM type).  The atom types are explained on this page:

Then as needed, select atoms and change their type, either (A) directly using the "setattr" command, e.g.

setattr a idatmType Car sel

... meaning change the selected atom(s) to type "Car"

or (B) indirectly using the Build Structure tool, Modify Structure section to specify the element, geometry and number of substituents (including H) of the currently selected atom atom.

Looking at your structure, I'm guessing you would need to change two C3 (sp3 carbon) to C2 (sp2 carbon), or all the carbons in the ring to Car, although that wouldn't make any difference for the purposes of hydrogen addition.

If you change the atom type the label will not automatically update, so you'd have to re-execute labeling to see the label change.  Then when the atom types are to your liking, add hydrogens.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 3, 2020, at 10:16 AM, Peter Palenchar <peter.palenchar at villanova.edu> wrote:
> Hi,
> I have an NAD coming from a PDB file.  When I add H to it, Chimera has issues with the nicotinamide ring.  It isn't seeing the ring as aromatic.  I've saved the NAD without adding H as a .mol2 file and tried to edit it so that it would be seen by Chimera as being aromatic, but it is still adding 2 H's to some of the C in the ring that only should one.  I've attached the mol2 file that I've edited.  
> I've also tried to edit the .mol2 file where I've changed the C in the ring to C.2 and changed the bonds to double bonds (e.g. N1N, atom 36, and C2N, atom 37, have a double bond, C2N also has a single bond to C3N, and C2N is assigned C.2, but when I add H Chimera still puts two H on C2N).
> I can add the H and then delete the extra ones in Chimera, but then the bond angle for the remaining H is wrong.  Ideally, I'd get Chimera to see the system as aromatic.  But I'll take any input on the best way to start with a structure like this and get Chimera to create something that is close to NAD.
> Thanks!
> Peter Palenchar
> <NADf1SC6_A_edited.mol2>_______________________________________________
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