Task 1 - Introduction to Pymol

Providing path to python binaries for whole script to run

import sys
sys.path.append("/home/tema/bin/pymol/lib/python3.4/site-packages/")

Importing pymol as python module. This is needed to control pymol from jupyter notebook.

import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]

import pymol
pymol.finish_launching()
from pymol import cmd,stored

Initializing the model:

loading model with PDBID: 1cll
showing bonds as lines
zooming on risidues 4 and 5
making 1000 frames of current state
save current frame as the key one

cmd.do('''
fetch 1cll, async=0
as lines, n. C+O+N+CA
zoom i. 4+5
mset 1 x1000
mview store''')

Creating list to store residues. Then iterate over residues and append them to list.

stored.r = [] 
cmd.iterate('1cll and n. CA','stored.r.append(resi)')

Creating color list - points from 1 to 0.5 with number of steps equal to number of residues.

Setting colors for residues - red chanel number derived form the colors list, blue and green set to 0.5 and 0.75 respectively.

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 %s' % i)
cmd.show_as('cartoon','all')

Create movie frames. For each residue i from 1 to 100, create keyframe where residues form i to i+7 are zoomed in.

for i in range(length):
    cmd.frame((10*i)+1)
    cmd.zoom( 'n. CA and i. %d+%d' % (i,i+7))
    cmd.mview('store')

Video saved in .mov format using ffmpeg converter. And then converted to HTML5 friendly mp4 H.264 format. Tutorial taken form here. The resulting movie:

Artemiy Polozhintsev educational site

Task 1 - Introduction to Pymol