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 >