Morph with Chimera

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Making a morph movie with UCSF Chimera is extremely easy. There are tutorials on the website [1], but here is an outline:

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.

2. Make the morph as described here [2]

3. Save the morph as PDB file - it will be NMR-style with multiple models.

4. Open the PDB file with morph in PyMOL.

5. There are plenty of tutorials and how to make a movie with PyMOL. A simplistic way is to check the "Ray trace frames" and "Cache frame images" in movie menu, hit the play, wait for PyMOL to render all the images (it will eat cpu until it's done) button and the File->Save Movie As->PNG Images. This will create the numbered sequence of PNG files.

6. Make the movie file with the following command (but of course there are other more GUIsh ways to do this)

ffmpeg -qscale 5 -r 20 -b 9600 -i image%04d.png movie.mpg