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[modeller_usage] Restricting parts of the protein to alpha helix



Dear modeller users,

my current project involves the refinement of an tertrameric protein, which is already an homology model generated with modeller. Now, I tried to refine the existing model, because its N-terminus should be alpha helical.
My strategy involved creating an alpha-helix and generating a new chimeric protein with this. Maybe my strategy is bad or do carry some failure. 
Searching your archives, I found no fitting topic. I hope this community might be able to help me with my issues. There must be a slightly more elegant way to receive an helical n-terminus. 

My strategy in detail:(all files/examples/scripts are shown below).

 In a first step I created an alpha-helix (22 AA) matching the N-terminal AA sequence of my template pdb. The helix was created based on an script tutorial I found here : http://salilab.org/modeller/wiki/Make%20alpha%20helix

 In a second step I created a pir file, which seems to cause the problems. I followed the Pir-format on the modeller webpage, but the python script exits pointig at problems in the pir file.

 At least a simple pythonscript should create my chimera.

I figured out, that there is a problem in the pir file. I don't know, how to
create four helices or assign the already created to all four monomers.
Thanks for all your help,
Kalavera


Information:
My Pir file in principle:(Original residues are masked)

>P1;My-PDB
structureX:My-PDB:1:A:82:D:::0.00:0.00
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/*

>P1;alpha-helix
structureX:alpha-helix:1: :22: :::0.00:0.00
-----------------------------------------------
-----------------------------------/
-----------------------------------------------
-----------------------------------/
-----------------------------------------------
-----------------------------------/
XAAAAAAAAAAAAAAAAAAAAA-------------------------
-----------------------------------/*

>P1;chimera
sequence:chimera:::::::0.00:0.00
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/
XAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/*


my *.py script:

from modeller.automodel import *   
from modeller import *

log.verbose()    
env = environ(rand_seed=-42)  

env.io.atom_files_directory = '.'
#env.io.hetatm = env.io.hydrogen = True

a = automodel(env,
              alnfile  = 'my_pir_file.pir',     
              knowns   = ('My-PDB','alpha-helix'),
              sequence = 'chimera')          
              
a.repeat_optimization = 1                  
a.starting_model= 1           
a.ending_model  = 1  
a.final_malign3d = True        
a.make()                            
a.energy(output='VERY_LONG')


Parts of My-PDB:


ATOM      1  N   MET     1       9.237 -14.594  13.390  1.00133.02       1SG   2
ATOM      2  CA  MET     1      10.424 -14.242  12.577  1.00133.02       1SG   3
ATOM      3  CB  MET     1       9.978 -13.883  11.150  1.00133.02       1SG   4
ATOM      4  CG  MET     1      11.111 -13.752  10.133  1.00133.02       1SG   5
ATOM      5  SD  MET     1      10.531 -13.360   8.454  1.00133.02       1SG   6
ATOM      6  CE  MET     1       9.496 -14.845   8.300  1.00133.02       1SG   7
ATOM      7  C   MET     1      11.086 -13.059  13.198  1.00133.02       1SG   8
ATOM      8  O   MET     1      10.511 -12.420  14.078  1.00133.02       1SG   9
ATOM      9  N   LEU     2      12.328 -12.738  12.784  1.00173.80       1SG  10
ATOM     10  CA  LEU     2      12.915 -11.582  13.388  1.00173.80       1SG  11
ATOM     11  CB  LEU     2      14.364 -11.293  12.962  1.00173.80       1SG  12
ATOM     12  CG  LEU     2      15.370 -12.347  13.459  1.00173.80       1SG  13
ATOM     13  CD1 LEU     2      15.119 -13.714  12.806  1.00173.80       1SG  1
.....
ATOM    634  CH2 TRP    82      -2.392 -10.968  17.703  1.00228.90       1SG 635
ATOM    635  C   TRP    82      -1.256  -4.168  15.227  1.00228.90       1SG 636
ATOM    636  O   TRP    82      -1.869  -3.238  14.636  1.00228.90       1SG 637
ATOM    637  OXT TRP    82      -0.880  -4.112  16.427  1.00228.90       1SG 638
TER     637      TRP    82                                               1SG 639
ATOM    638  N   MET    83      -9.978 -14.264   9.752  1.00140.79       2SG 640
ATOM    639  CA  MET    83     -11.395 -14.650   9.550  1.00140.79       2SG 641
ATOM    640  CB  MET    83     -11.772 -14.541   8.059  1.00140.79       2SG 642
ATOM    641  CG  MET    83     -11.766 -13.103   7.529  1.00140.79       2SG 643
.....








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