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Edit and run



In [1]:

    
import urllib2
import tempfile



In [2]:

    
import rosetta; rosetta.init()
from interface_fragment_matching import pdb_parsing



In [3]:

    
import ipython_glmol
from ipython_glmol.display_hooks import pose_display

Read pdb from rcsb and generate a rosetta pose.



In [4]:

    
with tempfile.NamedTemporaryFile() as tf:
    source_atoms = pdb_parsing.parse_pdb(urllib2.urlopen("http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1QYS").read())
    tf.write(pdb_parsing.to_pdb(source_atoms))
    
    source_structure = rosetta.pose_from_pdb(tf.name)
    source_structure.pdb_info().name("1QYS")

# Reset pdbinfo to align residue numbering
source_structure.pdb_info( rosetta.core.pose.PDBInfo(source_structure) )









    Out[4]:





<rosetta.core.pose.__pose_all_at_once_.PDBInfo at 0x53ddec0>

Display pose with sensible default representation.



In [5]:

    
from ipython_glmol.glmol_repr import Sphere, Line, Ribbon, Stick, ResidueSpectrum
from ipython_glmol.glmol_selectors import ResidueNumber, All, Heavyatom, Carbon



In [6]:

    
basic_repr = Line(Heavyatom()) + Stick( ResidueNumber[0:10] + Heavyatom())



In [7]:

    
pose_display(source_structure) + basic_repr









    Out[7]:



In [11]:

    
pose_display(source_structure) + ResidueSpectrum("residue_number", "gist_rainbow", sub_selector=Carbon()) + Ribbon() + Stick(Heavyatom())









    Out[11]:

Define representation based on pose data.



In [9]:

    
import interface_fragment_matching.utility.energies

scorefn = rosetta.getScoreFunction()
relax = rosetta.protocols.relax.FastRelax( scorefn, 1 )
relax.apply( source_structure )
scorefn( source_structure )









    Out[9]:





-169.3224091619103



In [10]:

    
pose_display( source_structure ) + ResidueSpectrum("total_score", "RdBu_r", sub_selector=Carbon(), thresholds=(-2, 0)) + Line(All() + Heavyatom())









    Out[10]: