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1.  Prepare your files.  Chimera may get a bit confused if sequence numbering is messed up, so remove all the things you don't actually need (e.g. waters) and make sure the initial and final conformation have perfectly aligned sequences.
 
1.  Prepare your files.  Chimera may get a bit confused if sequence numbering is messed up, so remove all the things you don't actually need (e.g. waters) and make sure the initial and final conformation have perfectly aligned sequences.
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2.  Make the morph as described here [http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/morph/morph.html]
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2.  Make the morph as described here [http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/morph/morph.html].  In a nutshell, activate Tools->Structure Comparison->Morph conformations, add the start and end structures (should be loaded into chimera first; if you want the morph movie run in a loop add the start model as the third item) and change the number of steps to 40 for smoother motion.
    
3.  Save the morph as PDB file - it will be NMR-style with multiple models.
 
3.  Save the morph as PDB file - it will be NMR-style with multiple models.
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