Build Structure Build Structure icon

Build Structure can generate atomic structures "from scratch" or modify existing molecules. See also: addaa, swapaa, swapna, combine, AddH, Rotamers, Minimize Structure, Metal Geometry, atom types, comparative modeling with Modeller

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:

Start Structure

The Start Structure section of Build Structure creates atoms, fragments, and molecules independent of any pre-existing atoms. 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 peptide 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 double-picking an atom (doubleclicking it with the button assigned to picking) and choosing Modify Atom from the context menu that appears.

Clicking Apply will change the selected atoms as specified:

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

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 choosing Adjust Bond from the context menu that appears when an bond is double-picked (doubleclicked with the button assigned to picking). Bonds can also be created and deleted with the command bond.

Clicking Apply will perform the chosen action:

Join Models

The Join Models section of Build Structure bonds two models and merges them into a single model. 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.

Clicking Apply replaces the two selected atoms with a bond and merges the models as specified:


UCSF Computer Graphics Laboratory / December 2010