Hello Neal, welcome

> 1) For the morphing/animation, do you use some models from the same
> protein and just show and hide them to make an animation ?

Yes, Jmol just displays in sequence whatever set of models is loaded 
into it. You can control speed, direction, repetition and range of 
models displayed.

 
> 2) Do you use MorphServer or something like that to create your 
> animation ?
> How your morphing method works ?

Ther is no morphing inside Jmol. You may get models that you have 
prepared using MorphServer, but Jmol bears no relation with that.




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