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 .....
Hie, you can simply use the constraints for secondary structure as describe in the online manual. See below the example given in it: # Example for model.build_sequence(), secondary_structure.alpha()
from modeller import * from modeller.optimizers import conjugate_gradients
# Set up environment e = environ() e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib')
# Build an extended chain model from primary sequence, and write it out m = model(e) m.build_sequence('GSCASVCGV') m.write(file='extended-chain.pdb')
# Make stereochemical restraints on all atoms allatoms = selection(m) m.restraints.make(allatoms, restraint_type='STEREO', spline_on_site=False)
# Constrain all residues to be alpha-helical # (Could also use m.residue_range() rather than m.residues here.) m.restraints.add(secondary_structure.alpha(m.residues))
# Get an optimized structure with CG, and write it out cg = conjugate_gradients() cg.optimize(allatoms, max_iterations=100) m.write(file='alpha-helix.pdb') other useful command in the online manual here: http://salilab.org/modeller/manual/
Best regards!
Kalavera@gmx.net a écrit :
> 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 > ..... > > > > > > > > > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
On 09/05/2011 06:23 AM, Kalavera@gmx.net wrote: > 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.
That should work, since Modeller builds models that look like the templates - it doesn't matter where the templates come from.
> 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.
Clearly you will need to fix this problem before you can proceed. If you can't figure out what the problem is with the Modeller log file in front of you (it usually gives you a pretty clear indication what the problem is) then it's unlikely anybody can help you *without* seeing that log file! If you can't figure it out, tell us what the error is.
Your Python script looks fine. Your alignment also looks OK, but note that your sequence is aligned both with your alpha-helical protein and the 'My-PDB' template. So Modeller will try to build a model which looks like *both* proteins. That's not going to work, since they have different secondary structures - align it with one or the other.
As Anthony points out, you can skip the intermediate step of producing an alpha-helical template and just include the alpha-helical restraints. The same consideration applies though - you will need to modify your alignment in this region so that your model does not align with My-PDB, otherwise the alpha-helical restraints will likely conflict with its secondary structure.
> I don't know, how to > create four helices or assign the already created to all four monomers.
If you mean you have this same helix in all four monomers, then you would need to add three more copies of the alpha-helical template aligned with each of the chains (so you'd have 5 templates in all). Anthony's solution would be cleaner here though.
Ben Webb, Modeller Caretaker
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Anthony Couvreux -
Kalavera＠gmx.net -
Modeller Caretaker