[modeller_usage] Restricting parts of the protein to alpha helix
To:
Subject: [modeller_usage] Restricting parts of the protein to alpha helix
From:
Date: Mon, 05 Sep 2011 15:23:33 +0200
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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