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 functional group identification, hydrogen addition, and hydrogen bond identification. Atom types also determine initial assignments of VDW radii. 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.
|IDATM atom type||description|
|N3+||N3+||sp3-hybridized nitrogen with formal positive charge|
|N3||N3||sp3-hybridized nitrogen, neutral|
|N2||Npl||sp2-hybridized nitrogen bonded to two other atoms near neutral pH (pyridine)|
|Npl||Npl||sp2-hybridized nitrogen bonded to three other atoms near neutral pH (trigonal planar; amide, aniline)|
|Ntr||Ntr||nitro group nitrogen|
|O3-||O-||resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, etc.)|
|O2-||O-||resonance-equivalent terminal oxygen on planar center (carboxylate, nitro, nitrate)|
|S3+||S3+||sp3-hybridized sulfur with formal positive charge|
|Sac||Sac||sulfate, sulfonate, or sulfamate sulfur|
|Son||Sox||sulfone sulfur (>SO2)|
|Sxd||Sox||sulfoxide sulfur (>SO)|
|B||Box||other oxidized boron|
|B||B||other boron (not oxidized)|
|P3+||P3+||sp3-hybridized phosphorus with formal positive charge|
|Pac||Pac||phosphate, phosphonate, or phosphamate phosphorus|
|HC||HC||hydrogen bonded to carbon|
|DC||DC||deuterium bonded to carbon|
|(element symbol)||(element symbol)||atoms of elements not mentioned above|
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:
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.