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Tool: Add Hydrogens

Add Hydrogens adds hydrogen atoms to atomic models, as well as OXT atoms where missing from peptide C-termini. The corresponding command is addh. See also: H-Bonds, Build Structure, Add Charges, Check Waters, Dock Prep

Add Hydrogens can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).

Add hydrogens to: The atomic model(s) to protonate should be chosen from the list.

The Method for adding hydrogens can be:

Clicking the Options button shows/hides additional options:

Protonation states: By default, if amino acids have standard residue names, each histidine sidechain will be protonated based on its local environment, whereas the sidechains of other residue types will be assigned protonation states reasonable at physiological pH, regardless of the local environment: negative aspartic acid and glutamic acid, positive arginine and lysine, and neutral cysteine and tyrosine. However, alternative protonation states of certain amino acids can be specified by changing their residue names beforehand (with setattr or by text-editing the input structure file):

Further options:

Clicking OK adds hydrogens and dismisses the dialog, while Cancel merely dismisses the dialog. Clicking Help shows this page in the Help Viewer.

The positions of pre-existing atoms are not changed, but any lone pairs and atoms of unidentifiable element are deleted. Hydrogens are named in accordance with the PDB standard, if possible, and positioned to produce the expected bond lengths. An attempt is made to preserve coloring schemes, coloring the added hydrogens by element (white) and/or to match their bond partners.

The default VDW radii of carbon, nitrogen, oxygen, and sulfur atoms depend on whether hydrogen atoms are present; thus, adding hydrogens will change the VDW radii of some atoms.

Protonation States

Add Hydrogens aims to generate protonation states reasonable for pH ~7 (such as in blood). For example, hydrogens are not added to the phosphodiester backbone of DNA and RNA, and in proteins, the default is to make aspartic acid and glutamic acid sidechains negatively charged and arginine and lysine sidechains positively charged. The following groups typically have pKa values near 7, however, so how they get protonated depends on the details of the structure:

Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected as needed:

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; Add Hydrogens 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:
Xatom types X-H bond length (Å)
sp3 carbon C31.0900
sp2 carbon C2,Car1.0800
sp carbonC1 1.0560
nitrogenN3+,N3,Npl,Ng+ 1.0100
sp3 oxygen O3
(except water)
sp3 oxygen O3
sulfurS3 1.3360
Bond lengths to other X are approximate, obtained by adding the covalent bond radii of elements X and H.

Recommended Alternative: Reduce

When a more intensive approach is desired, the program Reduce provided as part of MolProbity is a good alternative. It places hydrogens to optimize local H-bonding networks and avoid steric overlaps, while flipping certain sidechains 180° 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. The method is described in:

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.

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2022