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

CHIU,YEUNG adolphsdchiu at ufl.edu
Mon Jan 12 11:54:40 PST 2009

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

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