Animation Resources

• Chimera Animation notes

Animation Commands

• Animation Command Syntax

State Parameters and Transitions

Need to identify all the possible state parameters that can be changed between two states. All of those parameters need to be retained, probably in some form of immutable data type (tuple) within a dictionary for easy access to several parameter groups (viewer, volumes, surfaces, models, labels, etc.). Some of the elements in a state may have shared spatial parameters (e.g., molecular surfaces, molecules, and atoms may share a common spatial transform).

• Programming resources, including commonly used modules for access to molecular data attributes
• Animation State Parameters

Integrity Checking

Take a look at the code for chimera.update.checkForChanges(). This is related to c++ notification to python of object changes (using a 'modified atoms' list and another 'modified reasons' list). This may be helpful in checking the validity of state parameters and in automatically detecting changes for transitions.

Also, chimera.openModels.addRemoveHandler(func, data) might be used to add a trigger handler when removing models. This might be useful in the creation of a state instance as a way to maintain integrity or validity of the saved state. It may depend on whether the state instance keeps a reference or a copy of models in the saved state. For efficiency, it is better to keep a reference. For validity, it could be better to keep a copy. Perhaps a copy is required only when a model is removed, so the copy action could be triggered then. If a state instance that is registered as a handler is deleted, then call chimera.openModels.deleteRemoveHandler(handler) to delete the trigger handler.

Transitions

Molecular morphing

For example, morphing of 3por to 2por, see ​http://molmovdb.mbb.yale.edu/cgi-bin/morph.cgi?ID=009069-29776

This is probably handled already in Chimera. Should it be some kind of transition parameter for the animation extension?