[Chimera-users] Add Hydrogens - non standard residue - protonation state

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 18 16:12:39 PDT 2016

Hi Subha,
Chimera makes its best guess as to the atom types in a nonstandard residue, using the bond lengths and angles. In this case it did not figure out the atom type you expected.  You would need to correct the atom type of that N atom to what you want before adding hydrogens and to do so, you would need to know its atom name (or serial number, or some way of specifying it in the command).  There is no general way to specify the net charge of a nonstandard residue in the addh command.

The atom types in Chimera are described here:

…you can see the atom-type assignments as labels, for example if the molecule was model 3:

labelopt info idatmType
label #3

…and  can use the setattr command to change them, for example something like:

setattr a idatmType N2  #3 at N8
label #3

I understand you may not know ahead of time about which atoms will have this problem, but this is the only way I can think of to directly control the protonation state of atoms in nonstandard residues with a command.

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

> On Aug 18, 2016, at 3:22 PM, Subha Kalyaanamoorthy <kalyaana at ualberta.ca> wrote:
> Hi There,
> Can anybody please suggest me how to use 'setattr' (or any other function) to assign a protonation state for an atom in a non-standard residue. 
> I have a ligand and I am using a python script to add hydrogens and charge to the ligand molecule using chimera no-gui. I see that chimera adds an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1 to the molecule. Removing this hydrogen using GUI is simple but not practical for large set of molecules. So, it would be helpful if somebody suggest me a command-line to set specific protonation states for atoms (in non-standard residue).
> Thanks and Best Regards,
> Subha

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