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The 'peptide' set in Jmol matches a 'protein' that has between 2 and 12 residues. The purpose of this is to pick up alpha-carbon-only models If the group has exactly 1 atom whose name is CA then it is considered protein. If the group has 4 atoms named N, CA, C and (O or O1) and they are bonded in the correct order, then the group is considered protein. The atoms that make up the set are recognized by the names of the atoms. This has the advantage that modified groups and interesting things that are not amino acids can still be identified as part of the protein. It is independent of the group name and independent of whether the atoms are defined in ATOM records or HETATM records. The 'protein' set in Jmol is based solely on the atoms that make up the group.

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This will usually be the 20 canonical proteinogenic amino acids, plus ambiguous Asp/Asn (ASX), ambiguous Glu/Gln (GLX) and 'unknown' (UNK). This set is composed of all groups with one of these names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, UNK. This is based only upon group name and has nothing to do with the actual atoms that make up the group.

transitionMetal: from Sc to Zn, from Y to Cd, from Hf to Hg, from Rf to Cn.

metalloid: B, Si, Ge, As, Sb, Te (note it overlaps with both metal and metalloid).

nonMetal: H B C, Si N, P, As O, S, Se, Te F, Cl, Br, I, At noble gases.

Note: Jmol 10.2 has a bug by which it may read calcium as alpha carbon based on its ID, although identification by element name works properly. If this is absent, then it will interpret the 'atom name' field (columns 13-14) to deduce the element identity. On PDB format, Jmol will identify the element from columns 77-78 (element symbol, right-justified). Also, deuterium or _D, and tritium or _T. On Jmol 11, element symbol preceded by underscore can also be used: _C, _O, _H, _S, etc. Technical note: most of these are set in src/org/jmol/viewer/JmolConstants.java By element name Please note that many of these keywords only apply to file formats that specify a residue ID or group ID as part of the information for each atom (most typically, pdb and mmcif formats, designed for macromolecules). Among them, there are keywords for predefined atom sets. Jmol recognizes and uses several keywords or tokens for several purposes: commands in the scripting language, colors, etc. 3 Selecting atom sets from the pop-up menu.