AddH adds hydrogen atoms to structures. Chimera uses atom and residue names, or if these are not "standard," atomic coordinates, to determine connectivity and atom types; AddH then uses the atom types to determine the number of hydrogens to be added and their positions. The positions of pre-existing atoms are not changed. Any lone pairs or unidentifiable-element atoms will be deleted, however. AddH is also implemented as the command addh.
There are several ways to start AddH, a tool in the Structure Editing category. AddH adds hydrogens to all open molecule models, unless called with add hydrogens in the Model Panel when only a subset is chosen. If any atoms cannot be assigned a type, a dialog will appear. It is necessary to click on the line for each unassigned atom and then indicate its proper substituent geometry and number of substituents.
Bond lengths for X-H (X = C/N/O/S) are taken from the Amber parm99 parameters:
|X||atom types||X-H bond length (Å)|
The default VDW radii of carbon, nitrogen, oxygen, and sulfur atoms depend on whether hydrogen atoms are present. Therefore, the radii of some atoms will change when hydrogens are added.
AddH attempts to achieve protonation states reasonable at physiological pH; hydrogens are not added to the phosphodiester moieties of DNA and RNA, for example. Of the standard amino acid side chains, a negative charge state results for Asp (D) and Glu (E) and a positive charge state results for Arg (R), Lys (K), and His (H). While a neutral histidine side chain is also common, there are two neutral tautomers, NE-protonated and ND-protonated; addition of hydrogens to both NE and ND enables the user to choose to retain both or delete one or the other, based on examination of the surroundings.
Note that the determination of atom types is approximate, and especially if the resolution of the input coordinates is low, errors may occur. Unusual functional groups may pose a problem. Even when types are determined properly, the planarity of certain extended groups of atoms may not be maintained. There is no optimization to maximize hydrogen-bonding networks. Therefore, the resulting coordinates should not be interpreted as the energetically preferred positions of the hydrogens or used (directly) to draw conclusions about hydrogen-bonding patterns.
When a more intensive approach is desired, the program Reduce (developed by the Richardson Laboratory) is a good alternative. Reduce places hydrogens to optimize local H-bonding networks and avoid steric overlaps, while flipping certain sidechains 180 degrees as deemed appropriate to fulfill these criteria. Asparagine and glutamine sidechains may be flipped to switch their terminal N and O atoms, and the imidazole ring of histidine may be flipped to switch N and C identities. The protonation state of histidine is adjusted based on the local environment.
Reduce is available free at http://kinemage.biochem.duke.edu:
J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson, "Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation" J Mol Biol 285:1735 (1999).