Build Structure

Build Structure can generate atomic structures “from scratch” or modify existing molecules. See also: addaa, swapaa, swapna, AddH, Rotamers, Ramachandran Plot, Metal Geometry, Minimize Structure, Unit Cell, Multiscale Models, Change Chain IDs, Renumber Residues, Chimera interface to Modeller, atom types, modifying and saving data

There are several ways to start Build Structure, a tool in the Structure Editing category. Different sections are available from the menu near the top of the dialog:

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

Close dismisses the Build Structure tool; Help opens this manual page in a browser window.

Outside of Build Structure, atoms and bonds can also be deleted:

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

← Start Structure

The Start Structure section of Build Structure creates atoms, fragments, and molecules independent of any pre-existing atoms. See also: open (SMILES and PubChem), rna

Options are to Add:

• atom - a single atom; helium is used as a dummy type not bonded to other atoms. Placement options:
  • Center of view
  • specified coordinates x, y and z in the model coordinate system
  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 3D structure for the specified SMILES string. The structure is generated using the SMILES translator provided by the National Cancer Institute CADD group, or if that does not produce a structure, the smi23d web service provided by the cheminformatics group at Indiana University. The smi23d service deploys the same procedure as described for Pub3D 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.
• PubChem CID - a modeled structure from PubChem3D, specified by PubChem compound identifier (CID). PubChem3D includes most but not all PubChem Compound entries, e.g., only the parent forms of salts, and subject to limits on compound size, flexibility, and constituent atom types. Hydrogens are included, although it may be necessary to add or delete hydrogens to generate the desired protonation state.

• peptide - 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 2010 - Dunbrack 2010 smooth backbone-dependent rotamer library (5% stepdown; for chain-terminal residues, the Dunbrack 2002 backbone-independent version is used instead)
  • Dynameomics - Dyameomics 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.

• helical DNA/RNA - double-helical nucleic acid specified by the one-letter residue codes of one strand (capitalization does not matter); the complementary strand will also be built to generate a double helix. Possible types:
  • DNA (sequence containing A,T,G,C)
  • RNA (sequence containing A,U,G,C)
  • Hybrid DNA/RNA (enter DNA) (sequence containing A,T,G,C)
  Possible conformations:
  • A-form
  • B-form
  The geometries were derived by surveying known structures of double-helical nucleic acids. The same torsion angle values are used for a conformation regardless of the composition of the double helix (specific sequence and whether DNA, RNA, or DNA/RNA hybrid).
  
  
• more RNA... simply refers users to Assemble2, a Chimera plugin for designing 2D RNA structures and generating corresponding 3D structures. Executables, source code, and documentation are available for download.  Assemble2 is developed by Fabrice Jossinet (Institut de Biologie Moléculaire et Cellulaire, Strasbourg).

← 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 doubleclick-picking an atom when 0 or >3 other atoms are already selected, then choosing Modify Atom from the resulting context menu.

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).

Clicking Delete removes the selected atoms and bonds.

← 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 doubleclick-picking a bond when no other bonds are already selected, then choosing Adjust Bond from the resulting context menu. Bonds can also be created and deleted with the command bond, and bond lengths changed with the command adjust.

• Add/Delete
  • 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
  • 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
    Entering a new value or moving the slider will change the length. 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. Clicking Revert restores the selected bonds to their lengths prior to selection. Once the selection has been changed, however, the bonds can no longer be reverted, even if re-selected.

← Adjust Torsions

The Adjust Torsions section of Build Structure is a table of active (rotatable) torsions. Active torsions are saved in sessions. See also: rotation

There are several ways to start Adjust Torsions, a tool in the Structure Editing category. Torsions can be activated in three ways:

• Selecting exactly one bond, then clicking the Activate button on the dialog. With default mouse settings, a bond can be picked (selected from the graphics window) with Ctrl-click.
• Doubleclick-picking a bond when no other bonds are already selected, then choosing Rotate Bond from the resulting context menu.
• Using the rotation command.

Adjust Torsions - command-line specifiers

If the four atoms defining a torsion are called 1-2-3-4, 1 is the Near atom and 4 is the Far atom, which will move when the bond is rotated. The angle in degrees as defined by the current Near and Far atoms is shown in the Torsion column. Torsion can be toggled to Delta; the reported value is then the angle in degrees relative to the starting angle, and there are no Near and Far columns. For a terminal bond (lacking additional atoms on one end), the value shown is always a delta, even if the column header is toggled to Torsion.

A bond can be rotated by entering a new angle value (and pressing return), clicking the arrowheads flanking the angle value, or manipulating the dial. The Dial size can be set to small, medium, or large. Further, torsions can be manipulated in the graphics window with the mouse. This can be done by checking Rotate [torsion] using [button] and choosing the desired torsion and mouse button from the pulldown menus.

The Bond column contains a pulldown menu for each active rotation, labeled with identifiers for atoms 2->3 (those flanking the rotatable bond):

• Revert - restore the original torsion angle
• Reverse - change which side of the torsion moves when the bond is rotated (change the torsion definition from A-B-C-D to D-C-B-A)
• Deactivate - deactivate the bond rotation and remove it from the table. Note that the torsion will not automatically revert to its original value when deactivated; Revert should be used before Deactivate to retain the original torsional angle. Even if the same rotation is reactivated later, Revert will not work to restore the angle, since the original value has not been saved.
• Select - select the rotatable bond and deselect any others; when in the Torsion mode, also select the two flanking bonds if the rotatable bond is nonterminal

When atom 2 is bonded to more than two atoms, there is more than one possible Near atom, and alternatives (if any) are available in a pulldown menu from the current Near atom name. Likewise, when atom 3 is bonded to more than two atoms, there is more than one possible Far atom, and alternatives (if any) are available in a pulldown menu from the current Far atom name. For the first torsion in the example (figures above), there are two choices for the Near atom, C8 and C4, and two choices for the Far atom, O4' and C2'. For the second torsion, there are two choices for the Near atom, O4' and C3', and only one possible Far atom, O5'. Of course, if Reverse is used, the Near and Far choices are interchanged, and in the Delta mode, there are no Near and Far columns.

The Labels setting applies to all active torsions and can be switched among:

• None - no label
• ID - torsion ID number (the first column in the listing)
• Name - identifiers for atoms 2->3 (as shown in the Bond column)
• Angle - the angle in degrees

← 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 (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.
  • C-N length (default 1.33 Å)
  • Cα-C-N-Cα dihedral (ω angle) (default 180.0°)
  • C-N-Cα-C dihedral (φ angle) (default –120.0°)
    The existing ψ angle (N-Cα-C-N dihedral) of the same residue is simply reported; it can be changed as needed using Adjust Torsions.
  • Move atoms on [ selected N atom / selected C atom ] 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.

← Adjust Bond Angles

The Adjust Bond Angles section of Build Structure allows changing bond (valence) angles. Bond angles can also be changed with the command adjust.

First, two adjacent bonds defining an angle to be modified must be selected. The movement will be in the plane defined by the two selected bonds, and the Move [bond] side menu controls which set of atoms will move. While the selection exists, the bond angle can be modified by entering a new angle value (and pressing return), clicking the arrowheads flanking the value, or manipulating the dial. Revert restores the most recently changed bond angle to its original value, or if the moving side was switched after the angle was changed, the value at the time the moving side was switched. To preserve the ability to restore the original value, Revert to the original value before switching the side that moves.