Build Structure

Build Structure can generate atomic structures “from scratch” or modify existing molecules. See also: addaa, swapaa, swapna, AddH, Rotamers, Metal Geometry, Minimize Structure, Unit Cell, Multiscale Models, Change Chain IDs, Renumber Residues, atom types, comparative (homology) modeling, building and saving structures

There are several ways to start Build Structure, a tool in the Structure Editing category. It includes five sections shown as index cards:

• Start Structure - add an atom, fragment, or molecule not bonded to existing atoms
• Modify Structure - change existing atoms, build outward step-by-step from an existing structure
• Adjust Bonds - add bonds, delete bonds, change bond lengths
• Join Models - bond and merge two models, moving one of them to form the appropriate bond
• Invert - swap substituents, potentially changing chirality

Chimera does not include an “undo” function for building. Atoms can be removed:

• with the command delete
• by selecting them and using the menu item Actions... Atoms/Bonds... delete

Start Structure

The Start Structure section of Build Structure creates atoms, fragments, and molecules independent of any pre-existing atoms. Options are to Add:

• atom - a single helium atom, placed in the center of view. Helium is used essentially as a dummy type that is not bonded to other atoms. Select placed atom indicates the new atom should be selected. The Modify Structure section can then be used to specify the selected atom's element, valence, and geometry, and to append further atoms.
• fragment - the specified fragment, placed in the center of view. Several planar ring systems are available; a small diagram of the chosen Fragment is displayed.
• SMILES string - a modeled structure for the specified SMILES string, generated using the smi23d web service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University. This service deploys the same procedure used to populate the Pub3D database (below). Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.
• PubChem CID - a modeled structure specified by PubChem compound ID (CID), fetched from the Pub3D database using a web service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University. Pub3D is described in Willighagen et al., BMC Bioinformatics 8:487 (2007). About 99% of the compounds in PubChem are available; the structure generation pipeline generally handles organic compounds, but not inorganic, metallo-, or highly unstable species such as radicals. Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.

• peptide sequence - a peptide specified by one-letter amino acid codes (capitalization does not matter)

  Clicking Apply brings up another dialog for specifying backbone φ (phi) and ψ (psi) angles and other parameters. One or more rows can be chosen with the mouse and Set to values either entered manually or supplied for various types of secondary structure:

  description	φ (°)	ψ (°)
  α helix	-57	-47
  antiparallel β strand	-139	135
  parallel β strand	-119	113
  310 helix	-49	-26
  π helix	-57	-70

  Rows in the dialog can be chosen with the left mouse button. Ctrl-click toggles the state (chosen or not) of single line. A block can be chosen by dragging, or by clicking on the first (or last) line in the desired block and then Shift-clicking on its last (or first) line.

  Sidechain conformations will be taken from the specified Rotamer library:

  • Dunbrack - Dunbrack backbone-dependent rotamer library
  • Richardson (common-atom) - common-atom values (author-recommended) from the Richardson backbone-independent rotamer library
  • Richardson (mode) - mode values from the Richardson backbone-independent rotamer library
  The rotamer at each position will be chosen as described for the command swapaa with the criteria cp: by fewest number of clashes, and if a tie, then the highest probability according to the rotamer library. The residues are added in N→C order, so only clashes with more N-terminal residues are evaluated. The peptide will be assigned the specified chain ID.

  Clicking Apply (or OK, which also dismisses the dialog) creates the peptide. Hydrogen atoms are not included. Backbone bond lengths and angles are taken from the Amber ff99 parameters. Sidechain bond lengths and angles are taken from the Amber parameter files all*94.lib.

Modify Structure

The Modify Structure section of Build Structure can be used to change the element, valence (number of directly attached atoms), and/or geometry (spatial arrangement of attached atoms) of one or more selected atoms; hydrogens are appended as needed to fill the valence. Building outward can be done by successive cycles of modifying a hydrogen attached to the previously modified atom.

The Modify Structure dialog can be opened directly by double-picking an atom (doubleclicking it with the button assigned to picking) and choosing Modify Atom from the context menu that appears.

Clicking Apply will change the selected atoms as specified:

• Element - desired element
• Bonds - desired total number of substituents on the atom (0-4 allowed). Hydrogens will be added to the atom to generate the indicated total number of Bonds. Pre-existing atoms are not removed. If the atom is already bonded to one (and only one) other atom, the bond will be adjusted to an approximate length depending on the elements involved. The positions of any other atoms already present will not be changed. New hydrogens will be placed to form the target (idealized) bond angles, or if the atom already has two or more substituents, to maximally avoid those substituents. Bond lengths for X-H (X = C/N/O/S) are taken from the Amber parm99 parameters (see table). Bond lengths can be adjusted to specific values using Set Bond Length, or allowed to change along with other degrees of freedom during energy minimization.
• Geometry - target arrangement of bonds around the atom
  • linear - allowed for 2 bonds, target bond angle 180°
  • trigonal - allowed for 2-3 bonds, target bond angle(s) 120° in a plane
  • tetrahedral - allowed for 2-4 bonds, target bond angle(s) 109.5°

  In PDB format, atom names can be up to four characters long and should be unique within a residue. An atom name normally starts with the element symbol. If any element assignment would be changed, a new atom name or sequentially numbered range of names must be specified. When only atoms matching the specified element are selected, however, it is possible to retain their current names.

• Connect to pre-existing atoms if appropriate - if a newly added hydrogen would be very close to an existing atom in the same model as the selected atom, discard the hydrogen and form a bond to the existing atom instead
• Focus view on modified residue - focus the view on the the residue containing the modified atom
• Color new atoms by element - color the modified atom and any newly added hydrogens by element

• Residue Name
  • Leave unchanged
  • Change modified residue's name to [resname] - change the residue name to resname for all atoms in the residue, not just the modified atom (appropriate when a standard residue is modified; for example, a methylated lysine should no longer be named LYS)
  • Put just changed atoms in new residue named [resname] in chain [chainID] - put the modified atom and any new hydrogens in a new residue named resname in chain chainID; otherwise, they will be included in the atom's current residue

  In PDB format, residue names are normally three characters long and chain identifiers a single character (or blank). However, Chimera will tolerate four-character residue names, and the chain identifier can be specified as het or water (in PDB output, these translate to use of HETATM records with a blank chain identifier). Otherwise, PDB output will contain ATOM records for standard residues, HETATM records for nonstandard residues, and the specified chain identifier(s).

Adjust Bonds

The Adjust Bonds section of Build Structure allows adding bonds, deleting bonds, and changing bond lengths. This dialog can be opened directly by choosing Adjust Bond from the context menu that appears when an bond is double-picked (doubleclicked with the button assigned to picking). Bonds can also be created and deleted with the command bond.

Clicking Apply will perform the chosen action:

• Delete selected bonds - remove any bonds that are selected
• Add [option] bonds between selected atoms - add bonds to a selected set of atoms, where the option can be:
  • reasonable (default) - bond each pair in the set for which the interatomic distance is no greater than the sum of their covalent bond radii plus a tolerance of 0.4 Å
  • all possible - bond all pairs in the set, regardless of whether the bonds are reasonable
• Set length of selected bonds to [length] - adjust the lengths of the selected bonds sequentially to length Å, moving atoms on the:
  • smaller side (default)
  • larger side
  The order of bond adjustment may affect the final position of the structure (but not the structure itself) and cannot be controlled. If the bond is in a ring, only the flanking atoms will be moved, by equal distances in opposite directions. Besides clicking Apply, pressing Enter (return) in the length field is another way to change the length.

Join Models

The Join Models section of Build Structure forms a bond between two selected atoms. The two atoms must be in two different models, which will be merged into a single model when the bond is formed. See also: combine

• C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; 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.
  • C-N length (default 1.33 Å)
  • Cα-C-N-Cα dihedral (ω angle) (default 180.0°)
  • Move atoms on [ N / C ] side - which of the two models to reposition when forming the bond
  
  
• other bond - the more general case. One terminal atom (only bonded to one other atom) in each model must first be selected. These two atoms will be removed and replaced with the new bond. Usually these atoms will be hydrogens, so it may be useful to add hydrogens beforehand, to whole models with AddH or in a more local fashion with the Modify Structure section of Build Structure.
  • length - length for the new bond in Å
  • [menu of available dihedrals] dihedral - torsion angle in degrees for the four atoms in the dihedral chosen from the menu of possibilities
  • Move atoms on [model #] side - which of the two models to reposition when forming the bond

Invert

The Invert section of Build Structure allows exchanging 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. See also: invert, chirality

• If a single atom is selected, clicking Swap exchanges the positions of its two smallest substituents based on number of atoms, or if those are the same, atomic weights of the atoms directly bonded to the selected atom. Implicit hydrogens on the selected atom are considered, but not those on its substituents. These rules are not meant to reproduce the much more complex “priority” calculations used in chirality determination.
• If two atoms directly bonded to the same central atom are selected, clicking Swap will exchange the positions of the substituents rooted at those atoms.