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Command: build

Subcommands of build correspond to sections of the Build Structure tool:

See also: addh, bond, angle, torsion, delete, swapaa, swapna, altlocs, dockprep, combine, renumber, changechains, open, rna

build start atom  model-info  [ position  x,y,z ] [ resName  resname ] [ select  true | false ]
build start fragment  model-info   fragment-name  [ position  x,y,z ] [ resName  resname ]
build start peptide  model-info  sequence   φ11   φ22  ...  φNN  [ position  x,y,z ] [ chainId  ID ] [ rotLib   rotamer-library ]
build start nucleic  model-info  sequence  [ position  x,y,z ] [ type  dna | rna | hybrid ] [ form  A | B ]

For starting a new molecule with build start, the choices are atom, fragment, peptide, or nucleic. 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.

The model-info can be given as the identifier of an existing atomic model (for example, #2) or a character-string name for a new model.

The position of the new atom or new molecule's geometric center defaults to the current center of view, but can be given as x,y,z coordinates separated by commas only.

For fragment, both model-info and fragment-name are required. Several planar 5- and 6-membered rings and their fused ring systems are available, with choices for fragment-name as listed in the Build Structure dialog.

For peptide, the required arguments are model-info and 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 either 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

For nucleic, the required arguments are model-info and the sequence of one strand as a string of single-letter nucleic acid codes (upper- or lowercase). The complementary strand of the double helix will also be built according to the specified type (default dna) and form (default B). For building a hybrid DNA/RNA, the sequence of the DNA strand should be given. The nucleic acid chains will be assigned the first two unused chain IDs of the atomic model.

Further options:

Options for peptide only:

build modify  atom   element   numBonds  [ geometry  ion | single | linear | trigonal | tetrahedral ] [ connectBack  true | false ] [ colorByElement  true | false ] [ name  name ] [ newRes  true | false ] [ resName  resname ]
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 length of the bond will be adjusted depending on the elements involved. No other atoms are moved.

Other options:

build join peptide  atoms  [ length  bond-length ] [ phi  φ ] [ omega  ω ] [ move  large | small | C | N ]
The build join command forms a covalent bond of the specified geometry between two atomic models, combining the two models into one. The atoms of one model are repositioned and incorporated into the other model; the original model will no longer exist. Thus, it may be a good idea to save a session beforehand, since the join (along with other building actions) cannot be undone. The related command combine also combines atomic models, but without forming a bond or changing the relative positions of the atoms.

Currently, only a peptide bond can be formed, where atoms must include exactly one peptide C-terminal carbon atom C OR N-terminal nitrogen atom N (not both) from one model, and from a second model, exactly one of whichever of those two atoms is not in the first. These C and N atoms each must be bonded to only one carbon (except N in proline or hydroxyproline can be bonded to two carbons); however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond. The default length for the new C-N bond is 1.330 Å and the default omega angle (Cα-C-N-Cα dihedral) is 180.0°. There is no default for the phi angle (C-N-Cα-C dihedral). The model to move is repositioned and its atoms placed in the other model, using the chain ID from the other model. Options for which model to move:

The values of omega and phi (along with other peptide torsion angles) are attributes of the amino acid residue containing the newly bonded N.

build invert  atom-spec 

The build invert command exchanges the positions of two substituents of an atom, potentially inverting a chiral center. Substituents of atoms that are not chiral centers can also be swapped.

The results can be reversed by simply repeating the command.

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2023