Build Structure Build Structure icon

Build Structure can generate atomic structures “from scratch” or modify existing molecules. See also: addaa, swapaa, swapna, AddH, Rotamers, Metal Geometry, Minimize Structure, Unit Cell, Multiscale Models, Change Chain IDs, Renumber Residues, atom types, comparative (homology) modeling, building and saving structures

There are several ways to start Build Structure, a tool in the Structure Editing category. It includes five 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 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.


UCSF Computer Graphics Laboratory / November 2011