** This tool is in an early phase of development and is likely to
change significantly. **
Build Structure performs simple structure-building operations. 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 a general "undo" function for building. Atoms can be deleted using the Actions menu or the command delete.
See also: AddH, Adjust Torsions, Minimize Structure, Model Loops
The Place Atom(s) section of Build Structure creates atoms that are not bonded to any pre-existing atoms. It is mainly useful for starting a structure from scratch, because the Change Atom section can be used to append atoms to an existing structure. Currently, the only option is to place a single helium atom in the center of view. Clicking Place adds the atom with the specified Residue name. The atom can be made part of an existing molecule model (although it will not be bonded to anything) or a new model with a specified name. A new model will be assigned the lowest available model number.
The Change Atom section can then be used to specify element and valence, and to append additional atoms.
The Change Atom section of Build Structure appends atoms by filling the valence of a selected atom. It can be opened directly by double-picking an atom (doubleclicking it with the button assigned to picking) and choosing Change Atom from the context menu that appears.
The following must be specified for the selected atom:
The bond lengths used are reasonable but approximate. Bond lengths can be adjusted using Set Bond Length or Minimize Structure.
To build out further, one of the new hydrogens can be selected and the Change Atom process repeated.
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:
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).