The morph command creates a trajectory that morphs between two or more atomic models. The trajectory can be played back with the coordset command or the slider graphical interface. See also: making movies, the ChimeraX morphing highlight
Before morphing, the atomic models should be superimposed (such as with matchmaker). In the morph command, the models should be specified in the order desired for morphing. Although the same model number cannot be given more than once, a given structure can be opened multiple times to give copies with different model numbers. Examples:
morph #3,1,2 frames 40
morph #1.1-20 same t
morph #2,5 core 0.1 frames 30
Only the atoms in common among the input structures will be included in the resulting trajectory. 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 (see limitations).
Each sequential pair of input structures serves as the starting and ending points of one stage of the trajectory, and a morph trajectory can have multiple stages. Within each stage, intermediate sets of coordinates are generated:
The endpoint and intermediate coordinate sets are opened as a new trajectory model. The frames option (default N = 20) indicates generating N–1 intermediate coordinate sets per stage, giving a total number of frames in the trajectory = 1 + N(number of stages).
The same option indicates that the input structures have the same sequences, atom names, residue numbering, and chain IDs, as is typically the case for members of an NMR ensemble (default false, atoms paired as described below). Setting this option to true may make the calculation slightly faster, but otherwise there is little harm in staying with the default if there is any doubt as to whether numbering/naming are the same.
The hideModels option (default true) hides the input models, and the play option (default true) plays through the resulting trajectory a single time. Regardless of the play option, the coordset command and/or the slider can be used to replay the trajectory.
The slider option (default true) shows a graphical interface for trajectory playback. The slider can be dragged or a frame number entered directly. The interface also includes a play/pause button and another (marked with a red dot) for recording a movie. See also: coordset slider
method ( linear | corkscrew )
How to calculate the rigid-body transformations within a stage:
- linear - rotate the group of atoms around its centroid and translate it along the straight line between the initial and final positions of the centroid
- corkscrew (default) - move the group of atoms along a circular arc in the plane perpendicular to the rotation axis, and linearly along the rotation axis. When moving along the circular arc, the group rotates at the same rate as the tangent to the arc. The combination of circular and linear motion makes the centroid traverse a helical path between its initial and final positions. In general, if the rotation angle is small, the helical path will be nearly straight (a small segment on a cylinder of large diameter). In the case of the largest possible angle, 180°, the helical path turns by half a circle, and the helical axis passes through a point halfway between the initial and final centroids.
cartesian true | false
Whether coordinates within a group of atoms should be interpolated strictly in Cartesian space. Otherwise, internal coordinates will be used for the interpolation where possible. Using internal coordinates is slower but produces less distortion. A trajectory made with Cartesian forcing may be acceptable if few atomic details will be shown (for example, if only ribbons will be displayed).
How conformational changes within a stage are distributed across the trajectory, where the function can be:
- linear (default) - coordinate changes will be distributed approximately evenly
- ramp down - coordinates will change most rapidly near the starting conformation
- ramp up - coordinates will change most rapidly near the ending conformation
- sinusoidal - coordinates will change most rapidly halfway between the starting and ending conformations
colorSegments true | false
Hinges are identified using a reimplementation of the method described in Krebs and Gerstein, Nucleic Acids Res 28:1665 (2000). The coreFraction f (default 0.5) is the fraction of the residues in a chain to group in the first step of hinge detection. The best-matching fraction f of residues (best-fitting between the starting and ending structures) comprises one group and the remaining (1–f) a second group. Going through the residues in order, hinges are added between consecutive residues where there is a change from one group to the other, as long as a hinge is at least minHingeSpacing M residues away from the previous hinge (does not create a segment shorter than M residues, default 6). The colorSegments option shows the resulting segments in different colors (chosen automatically), whereas colorCore uses the specified color for residues in the initial core. Although segments are recomputed for each stage of a multistage morph, segment coloring only shows the first set.
Coordinate sets are generated by interpolating between starting and ending structures. Interpolation requires a pairing of atoms in the starting structure with atoms in the ending structure. Only atoms common to both stage endpoints are included in the morph trajectory.
The structures must contain equal numbers of biopolymer chains (see limitations). Unless same is true, atoms are paired as follows:
If the sets of chain IDs are identical (for example, each structure contains chains A and B), the IDs will be used to indicate pairing; if they differ (for example, one structure contains chains A and B, whereas another contains chains A and D), the chains will be paired by their order of occurrence in the input files. Residues are paired by aligning the chain sequences. The sequence alignment is performed using the matchmaker defaults (Needleman-Wunsch algorithm, BLOSUM-62 matrix, secondary structure reassignment with dssp, 30% secondary structure scoring, etc.), except that the Nucleic matrix is used for nucleic acids. Only the sequence alignment stage of matchmaker is performed, not the superposition of structures.
HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one “covalent” bond or pseudobond.
Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue. For example (disregarding hydrogens), phenylalanine and tyrosine have in common all atoms of phenylalanine.
Secondary structure is not automatically re-evaluated during playback. Protein cartoon (ribbon) display depends on which residues are in helices and strands, but these secondary structure assignments are not recomputed automatically as the coordinates change. The computeSS option of coordset or an alternative approach should be used to update the assignments.
Structures with different numbers of chains are not handled. Currently, a morph trajectory can only be generated from input structures with equal numbers of biopolymer chains. Extra chains in the input models should be deleted beforehand or split into separate models not used in morphing.
Sequences should be easy to align. The sequences of the structures must be aligned to determine the atoms in common for interpolation. When the sequences are dissimilar, parts of the sequence alignment may be wrong, leading to a jumbled and unattractive morph trajectory.