AddH

AddH adds hydrogen atoms to molecules, as well as OXT atoms where missing from peptide C-termini. 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, but any lone pairs and unidentifiable-element atoms are deleted. See also: FindHBond

There are several ways to start AddH, a tool in the Structure Editing category (including using it via Dock Prep). AddH is also implemented as the command addh.

Models to which hydrogens should be added can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Consider each model in isolation from all others - whether hydrogen placement should be affected by atoms within the same model only. Otherwise, other models in the vicinity (except submodels of the same model) may affect hydrogen placement, regardless of whether they were chosen for hydrogen addition.

The Method for adding hydrogens can be:

• steric only - based on atom types and clash avoidance
• also consider H-bonds (slower) (default) - based on atom types, clash avoidance, and hydrogen bond formation. Considering H-bonds increases the calculation time. Although hydrogens are placed to avoid clashes and form hydrogen bonds where possible, they are not energy-minimized, and a globally optimal network in terms of the number of H-bonds or total H-bonding energy is not necessarily found.

• Choices for histidine:
  • Residue-name-based (default) - residue names will be used to determine which histidine sidechain nitrogens should be protonated: the δ-nitrogen in residues named HID, the ε-nitrogen in HIE, and both nitrogens in HIP. Residues named HIS will be treated as unspecified, and may end up with either or both sidechain nitrogens protonated, depending on the method and the local environment.
  • Specified individually... regardless of which of the names above are used, the desired sidechain protonation state of each residue will be specified in a dialog by the user
  • Unspecified (determined by method) - regardless of which of the names above are used for histidine residues, all will be treated as unspecified, and may end up with either or both sidechain nitrogens protonated, depending on the method and the local environment.
• Choices for glutamic acid:
  • Residue-name-based (default) - residue names will be used to determine sidechain charge state: GLU negatively charged and GLH neutral, OE2-protonated
  • Specified individually... regardless of which of the names above are used, the desired sidechain protonation state of each residue will be specified in a dialog by the user
  • Charged - negatively charged
• Choices for aspartic acid:
  • Residue-name-based (default) - residue names will be used to determine sidechain charge state: ASP negatively charged and ASH neutral, OD2-protonated
  • Specified individually... regardless of which of the names above are used, the desired sidechain protonation state of each residue will be specified in a dialog by the user
  • Charged - negatively charged
• Choices for lysine:
  • Residue-name-based (default) - residue names will be used to determine sidechain charge state: LYS positively charged and LYN neutral
  • Specified individually... regardless of which of the names above are used, the desired sidechain protonation state of each residue will be specified in a dialog by the user
  • Charged - positively charged
• Choices for cysteine:
  • Residue-name-based (default) - residue names will be used to determine sidechain charge state: CYS unspecified and CYM negatively charged
  • Specified individually... regardless of which of the names above are used, the desired sidechain protonation state of each residue will be specified in a dialog by the user
  • Unspecified (determined by method) - regardless of which of the names above are used for cysteine residues, all will be treated as unspecified and the sidechain sulfur may be protonated or not depending on the method and the local environment.

If any atoms cannot be assigned a type, another 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.

Added hydrogens are colored the element color (default white) if the attached atom is colored by element, otherwise the same as the attached atom.

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.

Protonation States

AddH aims to generate protonation states reasonable at physiological pH. For example, hydrogens are not added to the phosphodiester moieties of DNA and RNA. By default, aspartic acid and glutamic acid sidechains are assumed to be negatively charged, arginine and lysine sidechains positively charged (although other states can be attained). Two chemical moieties are treated as ambiguous at biological pH:

• imidazoles such as histidine sidechains; histidine protonation states can be specified by the user or guessed by the method
• terminal phosphates (the third ionization); if one P–O bond is at least 0.05 Å longer than the others around that same phosphorus atom, that oxygen will be protonated

Residues at the ends of connected peptide chains are inspected to determine whether they are real termini, based on any SEQRES information in the input PDB file (or the mmCIF equivalent) and the presence or absence of additional chains with the same IDs. Real N-termini are assumed to be positively charged (⁺H₃N–) and real C-termini are assumed to be negatively charged (–CO₂^–). If a C-terminal carboxylate is missing an oxygen (OXT), it will be added. End residues that are not real termini are terminated like other chain-internal residues, with N(H)– and –C(=O). The position of the N-end “amide” hydrogen in such cases is not fully determined by the positions of the existing atoms; AddH places this hydrogen to produce a φ angle equal to that of the subsequent residue.

Bond Lengths

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)
sp3 carbon	C3	1.0900
sp2 carbon	C2,Car	1.0800
sp carbon	C1	1.0560
nitrogen	N3+,N3,Npl,Ng+	1.0100
sp3 oxygen	O3 (except water)	0.9600
sp3 oxygen	O3 (water)	0.9572
sulfur	S3	1.3360

Bond lengths to other X are approximate, obtained by adding the covalent bond radii of element X and H.

Recommended Alternative

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:

• for on-line use as part of the MolProbity service, on a file uploaded or chosen by PDB code (individual sidechain flips can be accepted or rejected)
• for download (from the Software section) to run on most platforms

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Word JM, Lovell SC, Richardson JS, Richardson DC. J Mol Biol. 1999 Jan 29;285(4):1735-47.