[Chimera-users] addH/removeH for charged a.a.

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 24 09:45:22 PDT 2006

Hi Dave,
Just use the AddH tool or the command "addh" to add hydrogens to your  

The residues are defined to give the most likely protonation states  
at physiological pH: lysine and arginine sidechains will be  
"protonated" (formal charge +1) and aspartic and glutamic acid  
sidechains will be "deprotonated" (formal charge -).  Protonation  
states are mentioned in the AddH man page:

If you actually wanted the less common neutral states, it is easy for  
lysine and arginine: just select (Ctrl-click) the hydrogen(s) you  
want to delete and use Actions... Atoms/Bonds... delete (or the  
command "delete sel").  For aspartic and glutamic acids, you would  
need to force the program to add a hydrogen that it normally  
wouldn't, which can be done but involves a longer explanation.  If  
you want that explanation, let me know.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 23, 2006, at 6:22 PM, Dave Roe wrote:

> Is there functionality that will
> - add a hydrogen (if needed) to all Lysines and Arginines to give the
>   protonated form
> - remove a hydrogen (if needed) from Aspartic and Glutamic acids to  
> give the
>   deprotonated form?
> -- 
> Dave Roe		roex0050 at umn.edu
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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