AddH

AddH adds hydrogen atoms to molecule models. 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.

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 add hydrogens to 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.

Even when only one model is chosen, hydrogen placement can be affected by other models perceived to interact with the chosen model. Different submodels of the same model are not considered to interact.

The Method for adding hydrogens can be:

• steric only - based on atom types and clash avoidance
• also consider H-bonds (slower) - based on atom types, clash avoidance, and hydrogen bond formation. 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.

• Residue-name-based - 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 for histidine residues, the desired protonation state of each histidine 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.

Clicking OK initiates hydrogen addition and dismisses the dialog, while Close merely dismisses the dialog. Help opens this manual page in a browser window.

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.

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.

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.

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

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).