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

[Elaine Meng]

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

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:
http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/addh/ 
addh.html

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


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
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users