Build Structure Build Structure icon

Build Structure can generate atomic structures "from scratch" or modify existing molecules. It is under development. See also: 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:

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:

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:

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). 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:

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:

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).

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 2008