[Chimera-users] "Extra" hydrogens in Dockprep and addH steps

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 12 13:05:33 PST 2009

Dear Yeung,
Chimera automatically identifies atom types using the input  
coordinates and bonding pattern.

In the case of the disulfide, the input structure is lacking the S-S  
bond.  You can either edit the input file (CONECT section) or just add  
the bond in Chimera before adding hydrogens.   You can add a bond by  
selecting the two atoms (Ctrl-click, Shift-Ctrl-click) and then using  
the command "bond sel" or the Build Structure tool (under Tools..  
Structure Editing.  See the Add/Delete Bonds section of Build  

Sometimes input bond lengths and angles are not very accurate, so that  
the types are harder to figure out, and some may be identified  
incorrectly. The number and location of hydrogens added to an atom  
depend on that atom's type.  Here are the explanations of the Chimera  
atom types:

As mentioned on the Dock Prep page,

the protonation states of any ambiguous groups and of those with  
possibly perturbed pKa values (for example, in active sites or  
coordinating metal ions) should be checked manually and corrected as  

If the result is just an extra hydrogen, you could simply select it  
with Ctrl-click and delete it (Actions... Atoms/Bonds... delete).  If  
it is missing hydrogens or wrong geometries (e.g. planar when you were  
expecting tetrahedral) then the fix is to delete any wrong-geometry  
hydrogens, change the atom types as needed (described below), and then  
add hydrogens again.  Charge assignment should be repeated after any  
manual correction of protonation states.

If you want to see what the atom types are:  Actions... Label... IDATM  

To change atom type, you can use the Build Structure tool, Modify Atom  
tab, or the command "setattr" -- for example, the following command  
would change the type of the currently selected atom(s) to N2:

setattr a idatmType N2 sel

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

On Jan 12, 2009, at 11:54 AM, CHIU,YEUNG wrote:

> Dear colleagues and friends,
> I notice that during "Tools -> Dockprep" and "Tools -> addH" steps
> Chimera sometimes will automatically add hydrogens to the
> positions considered necessary by the program itself. However,
> these positions do not always really have these hydrogens imposed
> on them.
> One situation is when I added hydrogen to the molecule containing
> nitrogen with lone-pair electrons, Chimera added hydrogen to the
> position of this lone-pair.
> One other situation is in the disulfide bond. It seems that
> Chimera can not recognize the disulfide bond, so hydrogen is added
> to each of the thiol group, which is obviously inappropriate.
> I'm wondering what causes these situations and how users can
> prevent them happening. Any help is appreciated. If you
> coincidently encountered with similar situation, I'm glad to hear
> your story as well~
> Happy new year and best wishes to your research!
> Sincerely yours
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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