I’m working on a Google summer of code project (gsoc) to add animation
features into libAvogadro, which provides the molecular viewer functionality
of Kalzium. My mentor is Marcus Hanwell, who worked on libAvogadro as a
gsoc project last summer.
As part of Kalzium as an educational tool, I think the ability to view
molecules in motion is a powerful tool for providing insight into how
biological functions happen.
My idea is to provide users with the ability to try different techniques for
motion generation of molecules (especially proteins) and be able to
visualize them with Kalzium. The current best system I’ve found for doing
this is VMD http://www.ks.uiuc.edu/Research/vmd/, developed at UIUC.
Below is a list of tasks I’ve outlined for the project. I’d love to get
feedback on what features developers and users might find useful.
The main goals are to implement task 1 (non-interactive motion) and task 3
(VCR-type functionality). I plan to start on task 2 (interactive motion)
only when the functionalities of task 1 and task 3 are well tested and
Task 1. non-interactive motion functionality. (This will involve using
OBMol’s support for multiple conformers.)
(a) implement ability to implement their motion generator by extending
classes in libAvogadro
(b) using part a, provide a file-input way to animate a molecule by reading
in files with coordinates of different conformers and displaying
© add support for some popular molecular simulation applications:
(examples rosetta, namd). Either use option (b), or some other. Options for
animation will differ on the type of simulation being done (Monte Carlo,
Task 2. interactive motion (i.e. a user can select an atom or residue and
(a) get user input for atom selection and vector for direction and magnitude
(b) decide how to pass information back to motion simulator (need to _gure
out the best way to do this type of communication, based on what was chosen
© add support for popular interactive molecular dynamics applications (ex
namd). This should be one chosen from one support was added for
non-interactive simulation for 1(a).
Task 3. VCR functionality
(a) fast-forward, rewind, play-back
(b) record to file to be played back in Kalzium
© record to some type of movie file that can be played in an external