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

[Dave Roe]

Thanks Elaine,
The key for me was that I needed to delete all hydrogens first and then use
the AddH tool.  It wouldn't remove the hydrogen from the acids if they were
already there.


* Elaine Meng <meng at cgl.ucsf.edu> [2006-08-24 09:45 -0700]:
> 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
> >
> >_______________________________________________
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> >Chimera-users at cgl.ucsf.edu
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> 
> 
> 
> 
> 

-- 
Dave Roe		roex0050 at umn.edu