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.
There are several ways to start AddH, a tool in the Utilities category. AddH adds hydrogens to any open molecule models. If any atoms cannot be assigned a type, a dialog box 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.
The default VDW radii depend on whether explicit hydrogen atoms are present. When there are no explicit hydrogens, the radii of some atoms are enlarged to compensate. When hydrogens are present, smaller radii are used for these atoms. Thus, the default radius of an atom may decrease 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 also pose a problem. Even when types are determined properly, the planarity of certain extended groups of atoms may not be maintained (the positions of input atoms are not changed, of course). There is no optimization of hydrogen positions to avoid clashes or maximize hydrogen-bonding networks. Therefore, results should not be used (directly) to examine hydrogen-bonding patterns or make statements about the energetically preferred positions of the hydrogens.