Atom Types in Chimera

Chimera uses atom and residue names, or if these are not "standard," the coordinates of atoms, to determine connectivity and atom types. This information is needed for identification of functional groups, addition of hydrogen atoms when they are not present, and identification of hydrogen bonds. The algorithm and atom types discerned are for the most part adapted from the program IDATM; for a detailed description of IDATM and validation testing, please see

"Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates," E.C. Meng and R.A. Lewis, J. Comp. 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 extensions 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. 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.