Build Structure

Build Structure can generate atomic structures "from scratch" or modify existing molecules. It is under development. See also: addaa, swapaa, swapna, combine, AddH, Rotamers, Minimize Structure, atom types

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

Add Atoms - create an atom, fragment, or molecule not bonded to existing atoms
Modify Atom - change existing atoms (element, valence, geometry), appending hydrogens as needed
Add/Delete Bonds
Set Bond Length

Only one card is shown at a time, and clicking the tab for another brings it to the front. Close dismisses the Build Structure tool; Help opens this manual page in a browser window.

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

Add Atoms

The Add Atoms section of Build Structure creates atoms, fragments, and molecules independent of any existing atoms.

Clicking Add generates the specified structure:

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 Atom section can then be used to specify the selected atom's element, valence, and geometry, 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 service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) 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 - fetch the modeled structure specified by PubChem compound ID from the Pub3D database provided by the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University. This database is described in Willighagen et al., BMC Bioinformatics 8:487 (2007). Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.

Atoms added with any of the above options are placed in a residue with the specified Residue name (normally three characters long in PDB format).

peptide sequence - generate the peptide specified by one-letter amino acid codes (capitalization does not matter).
Clicking Add 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.

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

The new atoms are placed in either an existing molecule model or a new model with a specified name. A new model will be assigned the lowest available model number. The new atoms are shown in the ball-and-stick representation and can be colored by element.

Modify Atom

The Modify Atom section of Build Structure can be used to change the element, valence (number of bonds), and/or geometry of one or more selected atoms; hydrogens are appended as needed to fill the valence. The Modify Atom 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 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).

To build out further, select one of the new hydrogens and use Modify Atom 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:

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

Bonds can also be created and deleted with the command bond.

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 bonds 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

The order of bond adjustment may affect the final position of the structure (but not the structure itself) and cannot be controlled.

UCSF Computer Graphics Laboratory / September 2009