In [1]:
from xmlrpclib import ServerProxy
In [2]:
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
In [3]:
import pymol
pymol.finish_launching()
from pymol import cmd, stored
In [5]:
cmd.fetch('1lmp')
Out[5]:
'1lmp'
In [6]:
cmd.do('''
fetch 1cll, async=0
as lines, n. C+O+N+CA
zoom i. 4+5
mset 1 x1000
mview store''')
In [7]:
for i in range(100):
    cmd.frame((10 * i) + 1)
    cmd.zoom('n. CA and i. %d+%d' % (i, i + 7))
    cmd.mview('store')
In [8]:
v = cmd.get_view()
cmd.set_view(v)
In [9]:
stored.r = [] 
cmd.iterate('1cll and n. CA', 'stored.r.append(int(resi))')
Out[9]:
152
In [10]:
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%d' %k, [colors[k], 0.5, 0.75])
    print [1, 1, colors[k]]
    cmd.set('cartoon_color', 'col%d' %k,'resi %d' %i)
cmd.show_as('cartoon', 'all')
In [11]:
cmd.png(filename='/tmp/pymol.png', width='10cm', dpi=300, ray=1)
In [12]:
import io
import base64
from IPython.display import HTML

video = io.open('gli.mp4', 'r+b').read()
encoded = base64.b64encode(video)
HTML(data='''<video alt="test" controls>
                <source src="data:video/mp4;base64,{0}" type="video/mp4" />
             </video>'''.format(encoded.decode('ascii')))
Out[12]: