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 Structure). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
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: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> As mentioned on the Dock Prep page, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.h...
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 needed. 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 type 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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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 CHIU,YEUNG
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