Subcommands of build correspond to sections of the Build Structure tool:
build start atom
[ position x,y,z ]
[ resName resname ]
[ select true | false ]
• build start peptide model sequence φ1,ψ1 φ2,ψ2 ... φN,ψN [ position x,y,z ] [ chainId ID ] [ rotLib rotamer-library ]
For starting a new molecule with build start, the choices are atom or peptide. With the open command, however, a wide variety of atomic structures for subsequent modification can be fetched from online sources or modeled from a SMILES string.• build modify atom element numBonds [ geometry ion | single | linear | trigonal | tetrahedral ] [ connectBack true | false ] [ colorByElement true | false ] [ name name ] [ resName resname ] [ newRes true | false ]
The model can be given as the identifier of an existing atomic model (for example, #2) or a character-string name for a new model.
For peptide, required arguments other than model are the sequence as a string of single-letter amino acid codes (upper- or lowercase) and a list of comma-separated pairs of φ,ψ values, one pair for each residue, in the same order as in the sequence. Even though the terminal residues lack φ or ψ, a pair of values is required for each residue. The “extra” values for the terminal residues will be ignored. Example:build start peptide "custom built" ADKLL -57,-47 -57,-47 -57,-47 -57,-47 -57,-47 rotLib Dunbrack
The position of the new atom or peptide geometric center defaults to the current center of view, but can be given as x,y,z coordinates separated by commas only.
Options for atom only:
- resName – a name for the new residue (default UNL)
- select – whether to select the new atom (default true), as may be convenient for subsequent modification
Options for peptide only:
- chainId – an existing or new chain ID (default the “lowest” unused ID)
- rotLib – which amino acid sidechain rotamer library to use (see swapaa for details and literature citations):
- Dunbrack (default)
The build modify command changes the type of a single specified atom and automatically fills its valence with attached hydrogens. The hydrogens could be modified in turn to continue building outward. The element (element symbol) and numBonds (total number of bonds to the atom, including hydrogens) must also be given, for example:build modify sel O 2 geometry tetrahedral
Hydrogens will be added to the atom to generate the indicated total number of bonds. They are added to form the idealized bond angles for the specified geometry, or if the atom already has two or more substituents, to maximally avoid those substituents. The default geometry is the same as for the atom's current type. Since the geometry around the atom may be changing, any pre-existing directly attached hydrogens are removed beforehand. No other atoms are removed automatically. If the atom is already bonded to one (and only one) other nonhydrogen atom, the bond will be adjusted to an approximate length depending on the elements involved. No other atoms are moved.
- connectBack (default true) – if a newly added hydrogen would be very close to an existing atom in the same model, discard the hydrogen and form a bond to the existing atom instead
- colorByElement (default true) – color the modified atom and any newly added hydrogens by element
- name – new name for the modified atom; if not given, the atom name is kept the same if the element stays the same, or changed to an element-based name if the element is changed
- resName – new name for the residue containing the modified atom (default UNK for amino acid in bonded chain, N for nucleic acid in bonded chain, UNL otherwise)
- newRes (default false) – whether to put only the new atom(s) in a new residue of the name given with resName instead of changing the name of the existing residue