[Chimera-users] Protonating Histidine Residues using Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 13 11:53:42 PST 2022

> On Jan 13, 2022, at 10:54 AM, Joshi, Keya <keyajoshi1996 at ku.edu> wrote:
> Hello Prof. Meng,
>                                Hope you are doing well and staying safe. My name is Keya Joshi. I am a second year PhD student in the department of Computational Biology at the University of Kansas. I am trying to use Chimera to protonate Histidine residue 816 in chain B. But I have no idea about how to do this using Chimera. 
>                                Can you please help me with this?
> With Regards
> Keya Joshi

Hi Keya,
I hope you are well, too!

(CC-ing the chimera-users at cgl.ucsf.edu address which is recommended for asking Chimera questions unless you are sending data that needs to remain private)

In the structure that you sent, histidine 816 in chain B is already protonated (already has hydrogens).  However, it is protonated to the neutral state.  Maybe you meant you wanted one more hydrogen to make it the positively charged state.

Two ideas:
(1) You can just use the AddH tool (menu: Tools... Structure Editing... AddH) or "addh" command to add hydrogens to the whole protein.  See help for information about the options:

On the PDB file that you sent, the default options of AddH (= simply using command "addh" without any other options) do add a hydrogen to 816 in chain B to put it in the positively charged state, but it also adds lots of other hydrogens including on carbons and on all of the other residues.  I don't know if that is a problem for you, or whether it is an improvement on the original structure.  Of course you can delete some hydrogens afterward, but it depends what you want.

(2) To just add one hydrogen to that sidechain nitrogen, instead use Build Structure (menu: Tools... Structure Editing... Build Structure), and in that tool change from "Start Structure" to "Modify Structure".  Select (Ctrl-click on) the nitrogen of His 816 that needs the hydrogen.  Selection is shown with a green outline on that atom. Then in  the tool, you want that selected atom to be N (stay the same element) but with 3 bonds and trigonal geometry as shown in the screenshot. Also as shown in the screenshot, choose the option to leave the residue name unchanged.  Then click Apply to add that one hydrogen.

... after I click Apply it looks like this:

about selection:

Build Structure tool:

You can find Chimera features using Chimera menu: Help... Search Documentation, e.g. to search for "hydrogens" or "building"

Our newer program ChimeraX also has an "addh" command.

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

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