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
This animation 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. NOTE: 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 requested, then the initial orientation is adjusted by applying the rotation around X with dX= −45 (i.e. − 90 / 2).
Below are two examples of rotation and rocking animation. In order to reduce the image file 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 corresponding image. The structure of sucrose-specific porin (PDB id 1a0s) was used to generate these images.
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. 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 C-terminus of the gap junction protein connexin-43 as an example (PDB id 1r5s).
NOTE: Model-based animation can be also generated using
In order to enlarge the view at an active site or other structural element, one
can specify the zoom level for the starting and ending
frames along with some increment to scale the view. The
settings for the initial
Last modified: Thu Feb 9 13:30:25 EST 2012