MD Movie does not automatically re-evaluate secondary structure. MD Movie does not automatically recompute secondary structure assignments as coordinates change across a trajectory. This is relevant when ribbons are displayed and the conformational changes are large enough to alter secondary structure assignments. To recompute secondary structure at each frame, use a per-frame script in MD Movie that includes the Chimera command ksdssp.

  Eric Pettersen
  UCSF Computer Graphics Lab
  http://www.cgl.ucsf.edu

On Oct 26, 2013, at 3:34 PM, "Kang, Yanyong" <Yanyong.Kang@vai.org> wrote:

Dear Chimera developer,

I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much

Best,

Yanyong

Dr. Yanyong Kang
Laboratory of Structural Sciences
Van Andel Research Institute
Tel, 616-234-5446

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