Atom Types in Chimera

Atom types are classifications based on element and bonding environment. Atom type assignments are used in functional group identification, hydrogen addition, and hydrogen bond identification, and to determine VDW radii.

Chimera uses atom and residue names, or if these are not "standard," the coordinates of atoms, to determine connectivity and atom types. Errors in atom-type assignment may occur, especially in low-resolution structures and unusual functional groups. Atom type assignments can be displayed as labels (for example, with Actions... Label... IDATM type) and changed with the command setattr.

The algorithm and atom types discerned are adapted from the program IDATM; for a detailed description of IDATM and validation testing, please see

E.C. Meng and R.A. Lewis, "Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates" J Comput Chem 12:891 (1991).

The atom types and algorithm, including extensions of the original method, are described briefly below. Where type definitions are not mutually exclusive, the atom is assigned the most specific type possible; for example, although a carboxylate carbon is also sp²-hybridized, it is assigned the Cac type. Since the categorizations in Chimera differ from those in the original method, the same type may appear in more than one row in the following table.

Atom-Type Identification Algorithm

Brief descriptions of the original algorithm and further steps added during implementation in Chimera are given here.

Many experimentally determined structures of molecules do not include hydrogen atoms. IDATM uses the coordinates of nonhydrogen atoms (plus any hydrogens, if present) to determine the connectivity and hybridization states of atoms within molecules. This knowledge is essential for detailed molecular modeling. The algorithm is hierarchical; the "easiest" assignments are done first and used to aid subsequent assignments. The procedure can be divided into several stages:

1. Heavy Atom Valence (HAV). Elements are determined from atom names, and atoms are considered bonded if the distance between them is no greater than the sum of their covalent bond radii plus a tolerance of 0.4 Å. Atoms are sorted according to the number of nonhydrogen atoms they are bonded to; this will be referred to as heavy atom valence.
2. Fully Determined Atoms and Atoms With HAV > 1. The types of some atoms may already be fully determined at this stage; for example, HAV 4 carbons must be sp³-hybridized. Distinctions are also made on the bases of number of attached oxygens. The average of the three bond angles about each HAV 3 atom is calculated and used to assign the type of the central atom. The average bond angle has been found to be a reliable indicator of hybridization state. Only one bond angle is available for HAV 2 atoms, and this is a less reliable indicator; HAV 2 carbon and nitrogen atoms are assigned types based on the angle but are marked for further examination.
3. Atoms with HAV = 1. The only geometric information available for HAV 1 atoms is bond length. Types are assigned based on bond length and the type of the partner atom.
4. Resolution of Ambiguities and Identification of Charged Groups. Atoms tagged for further examination in the second stage are retyped, if necessary, using bond length information. Next, functional groups likely to be charged at physiological pH are identified: sp³-hybridized nitrogens bonded only to sp³-hybridized carbons and/or hydrogens are assigned a positively charged type; guanidinium groups are identified; carboxylate and nitro groups are identified. Finally, isolated sp²-hybridized carbons (bonded to only sp³-hybridized atoms) are retyped as sp³-hybridized carbons.

In Chimera, a few additional distinctions are made. Carbons that are sp²-hybridized and part of planar ring systems are given an aromatic type. Oxygens within aromatic rings are given an aromatic type. Geometric criteria are used to subdivide sp²-hybridized nitrogens into double-bonded (or aromatic) and non-double-bonded categories. Sulfone and sulfoxide sulfurs are given two different types rather than lumped into a single category, as are resonance-equivalent terminal oxygens sharing formal negative charge.

Some types depend on protonation states, and more information is used to determine the protonation states of groups with pKa values close to 7:

• The types of nitrogens in histidine sidechains may be adjusted when AddH (or the command addh) determines histidine protonation states.
• When a phosphate group has three terminal oxygens (bonded only to the phosphorus), if one P–O bond is at least 0.05 Å longer than each of the others, that oxygen will be typed as O3 instead of O3–. A terminal O3 oxygen will be protonated if/when hydrogens are added, whereas terminal O3– oxygens will not.