[Chimera-users] "Extra" hydrogens in Dockprep and addH steps
meng at cgl.ucsf.edu
Mon Jan 12 13:05:33 PST 2009
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
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
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