Morph with Chimera

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]. 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.

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.

Alternatively, the following command

grep MODEL morph.pdb | sort -k2 -nr | sed -n 1p | awk '{for(i=1;i<=$2;i++) printf "set state, %d\nray 640,480\npng image%d.png\n",i,i;}' > pngmaker.pml

will create the pngmaker.pml which is the script file to run from pymol (after you loaded your morph.pdb and chose the presentation you want) to generate the sequence of 640x480 pixel ray-traced images.

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