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

Изучаем возможности Pymol на примере лизоцима (1LMP):

In [4]:
cmd.fetch('1lmp')
Out[4]:
'1lmp'
In [5]:
cmd.remove('solvent')

С помощью Sculpting можно вручную изменять структуру белка:

Сверху - исходная структура, снизу - измененная.

Мутация, которая приводит к потере связывания с лигандом:

In [6]:
cmd.reinitialize()
cmd.fetch('1lmp')
cmd.remove('solvent')
In [7]:
cmd.do('''
extract het, het
select env, byres /1lmp//A  and (het around 3.5)
show lines, env

''')
In [8]:
cmd.do('''
distance hbonds, /1lmp//A, het, 3.2, mode=2
label env and name ca, resn,resi

''')

Лиганд и его окружение, в связывании с лигандом участвует аспарагин 103.

In [9]:
from pymol import wizard
In [10]:
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
In [11]:
cmd.get_wizard().set_mode("ALA")
cmd.get_wizard().do_select("/1lmp//A/103")
cmd.get_wizard().apply()
cmd.set_wizard("done")

Лиганд и его окружение, участвующий в связывании с лигандом остаток заменен на аланин.

In [12]:
cmd.do('''

delete hbonds

hide lines

fetch 1lmp, 1lmp2


show sticks, het

show cartoons, 1lmp
show cartoons, 1lmp2

color yellow, 1lmp
color cyan, 1lmp2

color white, het


show sticks, /1lmp//A/ and resi 103
color orange, /1lmp//A/ and resi 103
show sticks, /1lmp2//A/ and resi 103
color blue, /1lmp2//A/ and resi 103


''')
In [13]:
cmd.remove('solvent')
In [14]:
cmd.do('''
set matrix_mode, 1
set movie_panel, 1
set cache_frames, 1
mset 1-150

frame 1
translate [0,60,0], object=1lmp2 
mview store                     
mview store, object=1lmp2         
mview store, object=1lmp

frame 60                        
translate [0,-60,0], object=1lmp2 
mview store                     
mview store, object=1lmp2         
mview store, object=1lmp        
mview interpolate, object=1lmp2 

frame 90                      
orient resi 103                        
mview store                     
mview store, object=1lmp2         
mview store, object=1lmp   

frame 120                       
orient resi 103                                       
mview store                     
mview store, object=1lmp2          
mview store, object=1lmp

''')
In [18]:
from IPython.display import HTML

HTML('<iframe src="https://player.vimeo.com/video/270170528" width="640" height="432" frameborder="0"></iframe>')
Out[18]:
In [16]:
cmd.reinitialize()
In [17]:
cmd.load('tamra.sdf')

---------------------------------------------------------------------------
CmdException                              Traceback (most recent call last)
<ipython-input-17-65a61948851a> in <module>()
----> 1 cmd.load('tamra.sdf')

C:\Users\User\Miniconda3\envs\molsim\lib\site-packages\pymol\importing.pyc in load(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, object_props, atom_props, _self)
    813                 kw['contents'] = _self.file_read(filename)
    814 
--> 815             return func(**kw)
    816         finally:
    817             _self.unlock(r,_self)

C:\Users\User\Miniconda3\envs\molsim\lib\site-packages\pymol\internal.pyc in _load(oname, finfo, state, ftype, finish, discrete, quiet, multiplex, zoom, mimic, plugin, object_props, atom_props, _self)
    394         if True:
    395             if ftype in _load2str:
--> 396                 finfo = _self.file_read(finfo)
    397                 ftype = _load2str[ftype]
    398             r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),

C:\Users\User\Miniconda3\envs\molsim\lib\site-packages\pymol\internal.pyc in file_read(finfo, _self)
    325         handle.close()
    326     except IOError:
--> 327         raise pymol.CmdException('failed to open file "%s"' % finfo)
    328 
    329     if contents[:2] == b'\x1f\x8b': # gzip magic number

CmdException:  Error: failed to open file "tamra.sdf"

Увы :(