Build Structure Build Structure icon

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:

Atomspec display style in the Labels preferences controls how atoms are listed in the Build Structure dialog: in the simple style (for example, HIS 16.A ND1, see also the Distances figure) or as command-line specifiers (for example, :16.A@ND1, see also the Adjust Torsions figure).

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:

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:

For any of the options above, clicking Apply will add the specified atom(s) and give them the specified Residue name (normally three characters long in PDB format). The new atom, fragment, or molecule can be colored by element and placed in an existing molecule model or a new model with a specified name. A new model will be assigned the lowest available model number.

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:

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

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.

Adjust Torsions Adjust Torsions icon

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:

Adjust Torsions - command-line specifiers
Adjust Torsions
An error message will appear if an attempt is made to activate a bond that is within a ring or already rotatable.

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.

bond rotation example 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):

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:

The places and Show degree symbol settings control how angle values are displayed when Labels is set to Angle. The Decimal places can be changed by clicking the arrowheads flanking the value.

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

Clicking Apply replaces the two selected atoms with a bond and merges the models as specified. The moved model will cease to exist as its atoms are merged into the other model. Chain identifiers and residue numbers may also be adjusted, in two phases. First, the two models are merged, and chain identifiers in the incoming (moving) model will be changed as needed to avoid duplication. Next, when the bond is formed, if only one side has a chain ID (excluding het), it will also be assigned to the other side, or if both already have an ID, the ID of the nonmoving side will be used for both. The chain whose ID changes will be renumbered as needed to avoid duplicate residue identifiers.

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

Any unintended results can be reversed by clicking Swap again without changing the selection.

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.


UCSF Computer Graphics Laboratory / May 2018