# @molecular-knot.txt

# Put this script into your PyMOL working directory.
# Run this script by typing @molecular-knot.txt into the PyMOL command line.

# This load command assumes that your file is named molecular-knot.pdb

load molecular-knot.pdb

# extract some atoms
# I extracted these atoms so that I can remove them from the final movie.

extract mol1, name F6CA+F6FA+F19+F7DA+F7DA+F113+P3CA
extract mol2, name O2
extract mol3, name P0FA+F7EA+F3EA+F1AA+F7CA+F1EA+F1AA
extract mol4, name P1+F58+F57+F1CA+F8DA+F58+F4CA+F0AA
extract mol5, name F6DA+F9CA+F6BA+F8EA+F0BA+F3+P39
extract Cl, name Cl2
extract cluster, name H203+H204+H20A+H20B+H20C+H20D+H20E+H20F+H20G+H20H+H20I+H20J+H20K+H20L+C200+C201+C202+C203+C204+C205+C206+C207

disable mol1 and mol2 and mol3 and mol4 and mol5 and cluster


# These viewport settings are for Instagram

viewport 640, 640

# create the ball and stick display
# I recreated this format from a picture I saw on the PyMOLwiki.

create molball, molecular-knot
color lightblue, molball
show spheres, molball
set sphere_scale, 0.25

show spheres, Cl

create molstick, molecular-knot
color skyblue, molstick
show sticks, molstick
set stick_transparency, 0.3
set stick_radius, 0.15

set valence, on
hide everything, molecular-knot
hide lines
hide lines, molball

color hydrogen, elem H and molball
color wheat, elem C and molball
color salmon, elem O and molball
color orange, elem Fe and molball
color lime, elem Cl
color lightblue, elem N and molball

# grey background gradient

set bg_gradient
set bg_rgb_top, grey55
set bg_rgb_bottom, grey05


# lighting

set specular, 0.25
set spec_power, 300
set spec_reflect, 0.5
util.ray_shadows("soft")

# higher quality ray tracing

set antialias, 1

# set up the view

viewport 640, 640
set orthoscopic, off
set field_of_view, 30
orient

# move the molecule a bit

rotate z, 51
zoom complete=1
translate [0,-0.4,0], state=0

# make a movie

mset 1 x120
movie.nutate(1,120,angle=30)

# If you want to view the movie in pymol, set ray_trace_frames=0, or it takes a long time for each frame.

set ray_trace_frames=1
set cache_frames=0
mclear

# move into a new directory where you want to save the png files. These directories should already exist.

cd ../1-movies/molecular-knot-2

# save the movie frames
# uncomment the line below to actually write the files. Remember to set ray_trace_frames=1 before writing the frames to disk.

# mpng molecular-knot-2

# Here are my ffmpeg settings:

# ffmpeg
#   -framerate 30     # input frame rate
#   -i image%03d.png  # image names (image000.png, ..., image999.png)
#   -s:v 640x640      # video size
#   -c:v libx264      # encoder
#   -profile:v main   # H.264 profile for video
#   -crf 12           # constant rate factor (0 to 23, 0 is lossless)
#   -pix_fmt yuv420p  # pixel format- changes the rgb from the pngs to yuv
#   -preset veryslow  # encoding speed (slow but higher quality per file size)
#   -tune stillimage  # tunes the encoding settings for images
#   -r 30             # output frame rate
#   output_file.mp4   # movie file name

# move into the directory that contains your png files before running the ffmpeg command.
# all together:
# ffmpeg -framerate 30 -pattern_type glob -i '*.png' -s:v 640x640 -c:v libx264 -profile:v main -crf 12 -tune stillimage -pix_fmt yuv420p -preset veryslow -r 30 molecular-knot-2.mp4