POLYVIEW-3D Tutorial
Part 7. Animation settings
This section concerns the settings that can be used to create
different animation effects, in particular rotation,
structure fluctuation, and zooming. These settings are
enabled only when the
animation
type of request is chosen. In
turn, options available within this field set are context
specific and become enabled depending on the selected type
of animation. The only universal option that applies to
all effects is a delay
between switching frames. However, the latter option has
some dependence on the type of animation. In particular,
if rocking effect is chosen within rotation, POLYVIEW-3D
introduces increased delays (minimum of 0.5 sec and two
times the pre-specified delay) at extreme positions. An
increased delay is also applied in the case of the first
frame in animations using structural models, and for the
starting and ending zooming frames.
Rotation
This animation effect allows one to see in detail all sides of the structure of interest. It is especially useful in conjunction with opaque rendering of molecular surfaces. Options available for this type of animation include the rotation angle increment (use smaller angle for smoother rotation effect) and axes to spin the structure around. Obviously, the smaller the angle increment, the larger the number of frames to be generated and the longer the time required to finish the job.
In addition to these options, one can request the rocking effect with the corresponding angle span for it. The rocking effect takes half of the time required for full rotation effect. When rocking effect is used, the initial orientation is adjusted automatically to place the original orientation in the middle of the animation. For example, if rocking around X axis with an angle span of 90 degrees is chosen, then the initial orientation is adjusted by applying a rotation around X with dX= −45 (i.e. − 90 / 2).
Below are two examples of rotation and rocking animations. In order to reduce the image size, they had been set to have the minimum number of frames with a wide angle increment. To see smoother rotation with refined settings, click on the respective image. The structure of sucrose-specific porin (PDB id 1a0s) was used to generate these images.
| Rotation around axes Y, Z | Rocking around X |
|---|---|
|
|
| Click on respective image to see options used for its rendering. | |
Models
When using multiple models, e.g. NMR-derived protein structures or docking models of protein complexes, one can generate a movie consisting of individual frames representing these models. By default, POLYVIEW-3D uses all models available to create this animation effect. However, it is also possible to specify how many first models should be taken into consideration.
Two images below represent animations of an ensemble of NMR conformations for the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein (PDB id 1aca): using all available models, in the first case, and first 5 models defined in the PDB file, in the latter case.
Animation using models can be also generated using
Trajectories and distortions
option from the
Advanced structure annotation
settings. The latter always takes all models available,
introducing extra delays for the first and last frames,
and generating reversible motion movies.
| Animate all models (Default option) |
Animate first 5 models |
|---|---|
|
|
| Click on respective image to see options used for its rendering. | |
Zoom
In order to enlarge an active site or other structural element, one
can specify the zooming for the starting and ending
structure along with some increment to scale the view. The
settings for the initial
zooming are located in
the Image settings
section. In general, the smaller the increment, the
smoother the effect obtained. By default,
zoom-in effect is
used. However, one can switch the effect to
zoom-out by
specifying the negative increment and reversing the
starting and ending scale values. Zooming is particularly
useful when coupled with
center of view option,
which is included in the
Overall structure view
section. Images below
demonstrate zoom in and zoom out
effect using the same protein as in the
ligands rendering section
(PDB id 1n9l).
| Zooming in (Default option) |
Zooming out | Zooming in Rebound animation |
|---|---|---|
|
|
|
| Click on respective image to see options used for its rendering. | ||