# Importing pymol module
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd,stored
# Fetching of 1cll
num_frames = 1000
cmd.reinitialize()
cmd.fetch('1cll', 'structure')
cmd.remove('hetatm')
cmd.bg_color('white')
cmd.color('silver')
cmd.zoom('1cll')
cmd.mset('1 x{0}'.format(int(num_frames)))
cmd.mview('store')
# List of CA atoms of amino acids in structure
stored.r = []
cmd.iterate('strucutre and n. CA', 'stored.r.append(resi)')
# Gradient coloring of amino acids
import numpy as np
length = len(stored.r)
colors = np.linspace(1,0.5, length)
for k,i in enumerate(stored.r):
cmd.set_color('col{}'.format(int(k)), [colors[k],0.9,1])
cmd.set('cartoon_color','col{}'.format(int(k)) ,'resi {}'.format(str(i)))
cmd.show_as('cartoon','all')
# What do we see?
import IPython
cmd.set('ray_trace_mode', 1)
cmd.png('pymol_rainbow.png', '1920', '1080', ray=1)
IPython.display.Image('pymol_rainbow.png', retina=True)
# Looping through residues
for i in range(length):
cmd.frame((10*i)+1)
cmd.zoom( 'n. CA and i. {0}+{1}'.format(int(i), int(i+7)))
cmd.mview('store')
# Saving 1000 frames
import os
cmd.set('ray_trace_mode', 1)
for i in range(num_frames):
cmd.frame(i)
cmd.png(os.path.join(os.getcwd(), 'pics', '{0}.png'.format(str(i))), '1920', '1080', ray=1)
%%bash
where_am_i=`echo $PWD`
ffmpeg -i "$where_am_i"/pics/%d.png -vcodec libx264 -crf 15 -hide_banner -loglevel panic "$where_am_i"/movie.mp4
from base64 import b64encode
from IPython.display import HTML
video = open('movie.mp4', 'rb').read()
encoded = b64encode(video)
HTML(data='''<video width=700px controls>
<source src="data:video/mp4; base64,{0}" type="video/mp4" />
</video>'''.format(encoded.decode('ascii')))