Build Structure

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

• Start Molecule - create atoms not bonded to pre-existing atoms
• Modify - change an atom's element, bond geometry, and valence, appending hydrogens as needed to fill the valence
• Add/Delete Bonds
• Set Bond Length

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 Molecule

The Start Molecule section of Build Structure creates atoms that are not bonded to any pre-existing atoms.

Clicking Add generates the specified atom(s):

• atom - place a single helium atom 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 section can then be used to specify the selected atom's element, bond geometry, and valence, and to append further atoms.
• fragment - place the specified fragment in the center of view. Several planar ring systems are available; a small diagram of the chosen Fragment is displayed.
• SMILES string - generate the specified structure. SMILES strings are converted to 3D structures using the smi23d web service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University. Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.
• PubChem CID - fetch the structure specified by PubChem compound ID from the Pub3D database provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University. Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.

The new atoms are placed in a residue with the specified Residue name (normally three characters long in PDB format), either in an existing molecule model or in a new model with a specified name. A new model will be assigned the lowest available model number.

Modify

The Modify section of Build Structure can be used to change the element, bond geometry, and/or valence of a selected atom; hydrogens are appended as needed to fill the valence. The Modify 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 Change adjusts the selected atom as specified:

• Element - target element of the atom
• Geometry - target arrangement bonds around the atom
  • ion - 0 bonds allowed
  • single - 0-1 bonds allowed
  • linear - 0-2 bonds allowed, target bond angle 180°
  • planar - 0-3 bonds allowed, target bond angle 120°
  • tetrahedral - 0-4 bonds allowed, target bond angle 109.5°
• Bonds - desired total number of substituents on the atom. 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 length of the bond to that atom will be adjusted; 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. The bond lengths used are reasonable but approximate. Bond lengths can be adjusted to specific values using Set Bond Length, or along with angles and other degrees of freedom using Minimize Structure.
• Name - atom name (normally starting with the element symbol and up to four characters long in PDB format); should be unique within a residue

• 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 atom(s) 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 atom(s) 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).

To build out further, select one of the new hydrogens and use Modify again.

Add/Delete Bonds

The Add/Delete Bonds section of Build Structure allows bond creation and deletion. Clicking Delete deletes any selected bonds. Clicking Add adds bonds to a selected set of atoms:

• all possible - bond all pairs in the set, regardless of whether the bonds are reasonable
• 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

Set Bond Length

The Set Bond Length section of Build Structure allows the lengths of one or more selected bonds to be set arbitrarily. This section can be opened directly by choosing Set Bond Length from the context menu that appears when an bond is double-picked (doubleclicked with the button assigned to picking).

• Set length of selected bond(s) to [b] - b is the desired bond length in angstroms; the selected bonds will be adjusted sequentially to this length after Enter (return) is pressed
• Move atoms on
  • smaller side (default)
  • larger side
  - which set of atoms should be translated when the bond length is adjusted; if the bond is in a ring, only the flanking atoms are moved, by equal distances in opposite directions