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:
- Remove - remove the conformation
- Up - move the conformation higher in the list
(earlier in the trajectory)
- Down - move the conformation lower in the list
(later in the trajectory)
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.
- Interpolation method - how the coordinates of intermediates
are determined. Hinge region identification and
screw axis determination are based on the descriptions in
Krebs
and Gerstein, Nucleic Acids Res 28:1665 (2000).
- corkscrew (default)
- the system is partitioned into groups of atoms separated by hinge regions.
Each group's starting and ending positions are related
by a rotation about a center chosen to describe as much of the movement
as possible, and a translation along the axis of rotation.
These two components are interpolated.
- independent
- the system is partitioned into groups of atoms separated by hinge regions.
Each group's starting and ending positions are related
by a rotation about the group's center of mass, and a translation.
These two components are interpolated.
- linear
- coordinates for each atom are interpolated
- Interpolation rate - how conformational changes will be distributed
across each segment
- 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
- Interpolation steps [K]
- each pair of input conformations will be
K steps apart (default 20); K–1
intermediates will be generated per segment
If Minimize is checked:
- Minimization steps [N]
- N steps of minimization (default 60)
will be applied to each intermediate
Before minimization can be performed, it is necessary to correct
structural inconsistencies, add hydrogens,
and associate atoms with
force field parameters.
Dock Prep,
AddH,
Add Charge, and
Minimize Structure
are called in no-GUI mode to perform these tasks; that is,
the dialogs will not appear, but each tool will execute with default
settings. When minimization is turned on, interpolation
to generate an intermediate will use the minimized coordinates
of the prior intermediate.
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:
- using MatchMaker
(or its command implementation,
mmaker),
which superimposes structures by constructing a sequence alignment and then
performing a least-squares fit of the aligned residue pairs
- using the
match command
to specify exactly which sets of atoms should be fit
- manipulating
models interactively, toggling their
activation states
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