Morph Conformations Morph Conformations icon

GTP binding switch
(1tag, 1tndA, morph intermediate)
transducin morph
Morph Conformations creates a trajectory that morphs between two or more structures. MD Movie is called to show the trajectory and can also be used to record it as a movie. The trajectory can be saved as a PDB file after it has been viewed. Morph Conformations is under development (see limitations).

There are several ways to start Morph Conformations, a tool in the Structure Comparison category.

The different structures should be opened as separate models or submodels in Chimera. They can have different numbers of residues (frequently seen in different structures of the same protein) or even different sequences, such as when homologs or mutants are compared. The structures must be superimposed.

The next step is to populate the Conformations list with structures; the order in the list corresponds to the order in which they 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 structures in the Conformations list will serve as the starting and ending points of one segment of a morph trajectory. A morph trajectory can have multiple segments. Within each segment, intermediates are generated by interpolating the positions of the atoms in common. Interpolation includes:
  1. rigid-body transformations of atom groups partitioned by hinge regions. Hinges are identified as described in Krebs and Gerstein, Nucleic Acids Res 28:1665 (2000).
  2. coordinate changes within the atom groups
How interpolated coordinates are generated, and in how many steps, can be specified independently for each segment. The following four settings apply to the segment preceding the structure currently highlighted in the Conformations list. The Minimize setting applies collectively to all segments of the morph trajectory: 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. Coordinates for the atoms in common from the segment endpoints (input structures) and the intermediates comprise the frames of the trajectory. The MD Movie tool can be used to record the trajectory as a movie file. After the trajectory has been viewed, it 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.

Superimposing Structures

The apparent motion across a morph trajectory depends on how the input structures are superimposed; matched regions will remain approximately steady.

There are several ways to superimpose structures in Chimera:

The first two methods allow iterative exclusion of poorly superimposed atoms from the fit.

Atoms in Common

Intermediates 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 segment endpoints are included in the morph trajectory.

Residues are paired by aligning the sequences of their chains. The sequence alignment is performed using the matchmaker defaults (Needleman-Wunsch algorithm, BLOSUM-62 matrix, secondary structure reassignment with ksdssp, 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. Morph Conformations does not change how the input structures are superimposed.

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.

Limitations

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. Additional chains should be deleted from the models to be used in morphing. However, these chains or the entire structures can be reopened as separate models.

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. A possible future improvement is to allow users to specify residue pairings with an input sequence alignment.

Minimization limitations. The Minimize Structure tool has its own set of limitations.

UCSF Computer Graphics Laboratory / April 2007