modeller_usage February 2006

modeller_usage@salilab.org

29 participants
29 discussions

nselat__596E> Atom index is out of range (iatm, natm)
by MGiò 01 Mar '06

01 Mar '06

Hi! I'm trying and model a 7-helix trans-membrane receptor, as I don't like the way MODELLER models my helices, while I highly appreciate its loop modelling, I've been using the "model-myini.py" input script to model my receptor starting from a initial.pdb containing the 7 helices already modelled. Every MODELLER run ends with the "nselat__596E> Atom index is out of range" error. Considering that this error changes the couple of atoms referring to any time I delete the corresponding residue in order to by-pass the error. I've attached to the mail the input files I used and the log file. Can you help me? best regards, MG

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symmetry on mod8v1
by Giovanni Grazioso 28 Feb '06

28 Feb '06

Dear Modellers, I'm building a pentamer with assial symmetry, I'm new on modeller 8v1 and my input doesn't work. Mod8v1 builds the pentamer but when starts the refinement this error occurred: defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:B', '211:B')) TypeError: defsym() got an unexpected keyword argument 'seg2' My input is: from modeller.automodel import * log.verbose() log.level(1, 1, 1, 1, 0) env = environ() env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = '*.pir', knowns = 'xxx', sequence = 'vvv') a.starting_model= 1 a.endind_model = 1 a.make() def defsym(mdl, aln, seg1, seg2): for (set, seg) in [(2, seg1), (3, seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) def defsym(mdl, aln, seg1, seg3): for (set, seg) in [(2, seg1), (4, seg3)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) def defsym(mdl, aln, seg1, seg4): for (set, seg) in [(2, seg1), (5,seg4)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) def defsym(mdl, aln, seg1, seg5): for (set, seg) in [(2, seg1), (6, seg5)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='ALL', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) # Generate five copies of a segment: code = 'xxx' mdl = model(env, file=code, model_segment=('1:A', '211:E')) aln = alignment(env) aln.append_model(mdl, align_codes=code, atom_files=code) aln.append_model(mdl, align_codes=code+'_ini', atom_files=code+'_ini') mdl.generate_topology(aln, sequence=code+'_ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.rename_segments(segment_ids=('A', 'B'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('B', 'C'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('C', 'D'), renumber_residues=(1, 1)) mdl.rename_segments(segment_ids=('D', 'E'), renumber_residues=(1, 1)) myedat = energy_data(dynamic_sphere = False) mdl.energy(edat=myedat) mdl.randomize_xyz(deviation=6.0) # Define the two segments (chains in this case) to be identical: defsym(mdl, aln, seg1=('1:A', '211:A'), seg2=('1:B', '211:B')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg3=('1:C', '211:C')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg4=('1:D', '211:D')) defsym(mdl, aln, seg1=('1:A', '211:A'), seg5=('1:E', '211:E')) # Make them identical by optimizing the initial randomized structure # without any other restraints: mdl.energy(edat=myedat) mdl.write(file='define_symmetry-1.atm') mdl.optimize(max_iterations=300, edat=myedat) mdl.write(file='define_symmetry-2.atm') mdl.energy(edat=myedat) # Now optimize with stereochemical restraints so that the # result is not so distorted a structure (still distorted # because optimization is not thorough): myedat.dynamic_sphere = True mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False, edat=myedat) mdl.randomize_xyz(deviation=3.0) for method in (1, 3, 1): # 1 = conjugate gradients, 3 = molecular dynamics mdl.optimize(max_iterations=300, md_return='FINAL', edat=myedat, optimization_method=method, output='REPORT') mdl.write(file='define_symmetry-3.atm') mdl.energy(edat=myedat) # Create a blank alignment so that superpose uses its 1:1 default aln = alignment(env) mdl = model(env, file='define_symmetry-3.atm', model_segment=('1:A', '211:A')) mdl2 = model(env, file='define_symmetry-3.atm', model_segment=('1:B', '211:B')) mdl3 = model(env, file='define_symmetry-3.atm', model_segment=('1:C', '211:C')) mdl4 = model(env, file='define_symmetry-3.atm', model_segment=('1:D', '211:D')) mdl5 = model(env, file='define_symmetry-3.atm', model_segment=('1:E', '211:E')) mdl.pick_atoms(aln, atom_types='MNCH') mdl.superpose(mdl2, mdl3, mdl4, mdl5, aln) Please, someone could help me telling where are the problems? Thank you very much. Giovanni

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ligands
by jo hanna 28 Feb '06

28 Feb '06

Hi In the advancde tutorial a model is built and refined and then the ligands added, is this the way the modelling should be done? or it is possible to build the model straight away around the ligands? Thanks Jo

2 1

reg:selecting the template.
by smitha vishwas 28 Feb '06

28 Feb '06

Hello all, Can any one tell me on what basis does the modeller is choosing the template for my query sequence? While the output of blast shows 3 options of more or less same scores but i got only one sequence while performing build profile in modeller. pls help. Regards Smitha. --------------------------------- Jiyo cricket on Yahoo! India cricket Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

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query??
by madhurima das 27 Feb '06

27 Feb '06

Dear Sir/Madam, I am using Modeller (Mod8V1 on OS X) to add missing residues to some pdb structures. While it worked for many structures, for some, I am getting an error (while reading the sequence (aligned) files: openf___224_> Open seq.ali str_sn5___E> increase MAXN: 15 Can anyone please tell me what is the problem? Looks like I have to increase some parameter MAXN. What is is this parameter and where and how can I increase it? Thanks, Yours sincerely, Madhurima Das Junior Research Fellow Bose Institute, Kolkata India. __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com

2 1

ask for your kindful help
by 典范 25 Feb '06

25 Feb '06

Hello everyone: Could you please tell me how to prepare the alignment(*.ali) file for modelling a protein-protein complex with known structures? thank you! Best regards, amber ly lidianfan(a)163.com 2006-02-26

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"Structure not read in" error
by Omid Khalouei 24 Feb '06

24 Feb '06

Hello, I am just starting to use Modeller. Even though I have a major in computer science, have used many bioinformatics tools, and am familiar with Python, I haven't been able to figure out how to run this program. To be honest I don't find it that user-friendly! Basically I'm not sure in which folder I have to put my alignment and PDB coordinate files. This is the alignment file that I have created but am not sure if it meets the specifications (they both refer to HIV-1 protease, residues 1 to 99 of chain A); P1;1A8GA structureX:1A8GA:1:A 99:A:.:.:.:. PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* P1;1ZPA sequence:1ZPA:1:A 99:A:.:.:.:. PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* The error message that I'm getting is "Structure not read in: 1" and it's raised from the Modeller8v1\modlib\modeller\util\top.py file. I would appreciate your help on this. Omid K.

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query
by abhilasha kirti 24 Feb '06

24 Feb '06

Sir we have just now started working with modeller.we would like to have step wise guide for preparing input file and running modeller,as in the manial also it is not mentioned so clearly. Please do the needful,we will be ever greaful to u. Thanking u Abhilasha __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com

2 1

pls help me to identify.
by smitha vishwas 24 Feb '06

24 Feb '06

hi all, I have modelled a protein using modeller & opted for 5 structures. but of those how do i identify the better one. pls help. Regards smitha --------------------------------- Jiyo cricket on Yahoo! India cricket Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

2 1

modeller ga341 score
by jo hanna 23 Feb '06

23 Feb '06

Hi After having built my models, i have decided to assess them using the ga341 score. the script i am using is: # Example for: model.assess_ga341() env = environ() # Read a model previously generated by Modeller's automodel class mdl = model(env, file='.59.pdb') # Set template-model sequence identity. (Not needed in this case, since # this is written by Modeller into the .pdb file.) mdl.seq_id = 30.174 score = mdl.assess_ga341() the ouput of this script for two different models is: model1 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.270804 Native energy (pair) : -225.273799 Native energy (surface) : -13.946407 Native energy (combined) : -6.357012 Z score (pair) : -9.813731 Z score (surface) : -7.147611 Z score (combined) : -11.464915 GA341 score : 1.000000 model2 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.256617 Native energy (pair) : -268.422282 Native energy (surface) : -16.727187 Native energy (combined) : -7.618686 Z score (pair) : -9.969647 Z score (surface) : -7.755271 Z score (combined) : -12.156111 GA341 score : 1.000000 how do i interpret these outputs? should both scores be 1? Jo

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modeller_usage February 2006