Morphing has limitations and the command is difficult to use. The morph command has been improved significantly in ChimeraX, so users may want to take a look at that program instead.
Morph is the command-line implementation of Morph Conformations; it creates a trajectory that morphs between two or more structures (see example systems). The method is based on that used by the Yale Morph Server:
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Krebs WG, Gerstein M. Nucleic Acids Res. 2000 Apr 15;28(8):1665-75.
Each sequential pair of input structures serves as the starting and ending points of one segment of the trajectory, and a morph trajectory can have multiple segments. Only the atoms in common among the input structures will be included in the morph trajectory.
By default, the MD Movie dialog will appear for showing the trajectory and optionally recording it as a movie. However, that dialog is suppressed when Chimera is in nogui mode or the nogui true option of morph movie is used, in which case the trajectory can be played with coordset instead. See also: vop morph, play, making movies, the ParM filament tutorial at the Chimera website
The different structures should be opened as separate models or submodels in Chimera and superimposed. The atom-spec given in a morph command may refer to a whole molecule model or a subset of the atoms in a model, but either way, the entire model will be used. The models can have different numbers of residues or different sequences (homologs or mutants can be compared), but currently they must contain equal numbers of chains. Chains are paired by chain ID if the sets of IDs are identical, otherwise by order of occurrence in the input files. Extra chains in the input models should be deleted beforehand or split into separate models not used in morphing.
The morph start command specifies the first structure (molecule model) in the trajectory and how to interpolate from that structure to the next. The entire molecule model containing the specified atoms will be used; atoms from more than one model should not be specified. A morph-name can be assigned with the name keyword, but is not necessary unless multiple morph trajectories will coexist. The default morph-name is default. All keywords to morph and their values except morph-name can be truncated to unambiguous strings.
The morph interpolate command specifies the next structure (molecule model) in the trajectory and how to interpolate from that structure to the one after it, if any. Since a morph trajectory can contain multiple segments, this command can be used multiple times for the same trajectory.
For both morph start and morph interpolate, additional options are:
| Option keyword | Possible values (see details) |
Defaults | |
|---|---|---|---|
| start | interpolate | ||
| method | corkscrew independent linear |
corkscrew | (same as preceding segment) |
| rate | linear "ramp down" "ramp up" sinusoidal |
linear | (same as preceding segment) |
| frames | (integers) | 20 | (same as preceding segment) |
| core | >0.0–1.0 | 0.5 | (same as preceding segment) |
| cartesian | true false |
false | false |
The morph movie command creates the trajectory. Normally MD Movie is started automatically to show the trajectory, but if Chimera is in nogui mode or the nogui true option is given, the MD Movie dialog is suppressed, and the command coordset can be used to play the trajectory instead. Whether to energy-minimize every interpolated conformation can be specified with minimize (default false, no minimization), and how many minimization steps to perform on each can be specified with step nsteps (default 60). Note that minimization has its own set of limitations and increases computational demands significantly.
The morph done command deletes the trajectory and exits from MD Movie.