Morph Conformations

Morph Conformations creates a trajectory that morphs between conformations of a molecule or a system of molecules. MD Movie is called to show the trajectory and can also be used to record it as a movie. After all frames have been viewed, the trajectory coordinates can be saved as a PDB file.

Currently, the structures (conformations) to morph between must contain identical sets of atoms. Unless the conformations are already well superimposed, it is necessary to superimpose them and save the matched coordinates before they can be used for morphing (see details).

There are several ways to start Morph Conformations, a tool in the Structure Comparison category. The conformations should be opened as separate models or submodels in Chimera.

The next step is to populate the Conformations list with models; the order in the list corresponds to the order in which the conformations will be visited in the output trajectory. Clicking Add... brings up a dialog that lists the open molecule models. Clicking a model's name and then the Add button (or double-clicking the model's name) puts it in the Conformations list. The same model can be added more than once to produce a morph trajectory that visits the same conformation more than once. After the desired conformations have been added, the model-choosing dialog can be dismissed by clicking Close.

Clicking a line in the Conformations list designates that entry as the target of subsequent button actions:

Each sequential pair of input conformations will serve as the starting and ending points of one segment of a morph trajectory. A morph trajectory can have one or more segments. Within each segment, intermediate states are obtained by interpolating between the starting and ending points. If Minimize is checked: Clicking Create hides the dialog (unless the option to Keep dialog up after Create is checked) and initiates the calculation. The MD Movie tool will be called to display the morph trajectory, and any specified Action on Create will be performed: The trajectory will be opened as a separate model, including separate copies of the original input conformations. The MD Movie tool can be used to record the trajectory as a movie file. After all frames have been viewed, the trajectory coordinates can be saved as a PDB file.

Hide hides the Morph Conformations dialog, Quit exits from the tool, and Help opens this manual page in a browser window. If the Morph Conformations dialog has been hidden or becomes obscured by other windows, it can be resurrected with the Raise option for its instance in the Tools menu.

Superposition Details

Sometimes conformations are already superimposed. Frequently, however, it will be left to the user to match the structures. Which parts of structures should be superimposed depends on the desired outcome; matched parts will remain approximately steady in the morph trajectory.

There are several ways to superimpose structures in Chimera:

The first two methods allow iterative exclusion of pairs of atoms that are far apart.

Because Morph Conformations uses the untransformed coordinates, superimposed structures must be saved and then reopened to be used as input. The matched model(s) should be saved either as transformed coordinates or relative to a consistent reference model. For morphing purposes, the structures can be saved as multiple PDB files (read in as separate models) or as a single PDB file (read in as submodels of the same model).


UCSF Computer Graphics Laboratory / October 2006