- modeller_usage - salilab.org

Advice on Modeller usage
by Nagesh Chakka 06 Mar '06

06 Mar '06

Hi, I am trying to use Modeller to obtain a model using the structure 1XU0. I have created the three files needed for Modeller Atom file http://www.rcsb.org/pdb/navbarsearch.do?newSearch=yes&isAuthorSearch=no&rad… Alignment file >P1;1XU0 structureX:1XU0:125:A:226:A:::: IGGYMLGNAVGRMSYQFNNPMESRYYNDYYNQMPNRVYRPMYRGEEYVSEDRFVRDCYNM SVTEYIIKPAEGKNNSELNQLDTTVKSQIIREMCITEYRRGS * >P1;XlPrP2 sequence:XlPrP2:1::134::::: IGGYMLGNAVGRMNHHFDNPMESRYYNDYYNQMPDRVYRPMYRSEEYVSEDRFVTDCYNM SVTEYIIKPSEGKNGSDVNQLDTVVKSKIIREMCITEYRRGS Top file INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'inputAlignment_files/prp2StructAli.txt' SET KNOWNS = '1XU0' SET SEQUENCE = 'XlPrP2' SET ATOM_FILES_DIRECTORY = '/home/nagesh/modelling/structure' SET STARTING_MODEL = 1 SET ENDING_MODEL = 4 CALL ROUTINE = 'model' In doing so, the final model XlPrP2.B99990004 does not contain all the atoms for a particular residue. For example, the following is the part of the model for one amino acid ATOM 1 N ILE 1 14.910 4.779 7.839 1.00 41.08 1SG 2 ATOM 2 CA ILE 1 13.848 4.061 8.581 1.00 41.08 1SG 3 ATOM 3 CB ILE 1 12.918 3.371 7.630 1.00 41.08 1SG 4 ATOM 4 CG2 ILE 1 11.924 2.529 8.447 1.00 41.08 1SG 5 ATOM 5 CG1 ILE 1 12.242 4.416 6.730 1.00 41.08 1SG 6 ATOM 6 CD1 ILE 1 11.473 3.813 5.557 1.00 41.08 1SG 7 ATOM 7 C ILE 1 14.422 3.050 9.510 1.00 41.08 1SG 8 ATOM 8 O ILE 1 15.261 2.235 9.128 1.00 41.08 1SG 9 Atoms from the structure file ATOM 1 N ILE A 125 15.197 -5.772 -0.208 1.00 0.00 N ATOM 2 CA ILE A 125 14.432 -5.479 0.993 1.00 0.00 C ATOM 3 C ILE A 125 14.890 -6.453 2.086 1.00 0.00 C ATOM 4 O ILE A 125 14.874 -7.667 1.884 1.00 0.00 O ATOM 5 CB ILE A 125 12.922 -5.586 0.661 1.00 0.00 C ATOM 6 CG1 ILE A 125 12.526 -4.523 -0.390 1.00 0.00 C ATOM 7 CG2 ILE A 125 12.073 -5.416 1.930 1.00 0.00 C ATOM 8 CD1 ILE A 125 11.131 -4.703 -1.000 1.00 0.00 C ATOM 9 H ILE A 125 14.783 -6.386 -0.892 1.00 0.00 H ATOM 10 HA ILE A 125 14.656 -4.459 1.305 1.00 0.00 H ATOM 11 HB ILE A 125 12.723 -6.575 0.246 1.00 0.00 H ATOM 12 1HG1 ILE A 125 12.591 -3.543 0.075 1.00 0.00 H ATOM 13 2HG1 ILE A 125 13.228 -4.540 -1.223 1.00 0.00 H ATOM 14 1HG2 ILE A 125 12.338 -4.494 2.447 1.00 0.00 H ATOM 15 2HG2 ILE A 125 11.014 -5.400 1.691 1.00 0.00 H ATOM 16 3HG2 ILE A 125 12.237 -6.268 2.586 1.00 0.00 H ATOM 17 1HD1 ILE A 125 10.989 -3.972 -1.797 1.00 0.00 H ATOM 18 2HD1 ILE A 125 11.032 -5.707 -1.414 1.00 0.00 H ATOM 19 3HD1 ILE A 125 10.362 -4.542 -0.250 1.00 0.00 H What is the reason for the loss of the atoms and how can I fix this. Thank you very much in advance Nagesh

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symmetry on mod8v2 - part 2
by Giovanni Grazioso 03 Mar '06

03 Mar '06

Thanks for your last reply, now the script (concerning the symmetry models) works well but after a few minutes the calculation ends with the following message on the log file: << end of ENERGY. runcmd______> restraints.make((def)residue_span_range=(0, 99999), (def)residue_grouping=1, restraint_type='stereo', (def)restraint_sel_atoms=1, (def)restraint_group=26, (def)basis_pdf_weight='LOCAL', (def)distance_rsr_model=1, (def)maximal_distance=999.0, (def)basis_relative_weight=0.050000000000000003, spline_on_site=False, (def)residue_span_sign=True, (def)intersegment=True, add_restraints=True, (def)dih_lib_only=False, (def)spline_dx=0.5, (def)spline_min_points=5, (def)spline_range=4.0, (def)mnch_lib=1, (def)accessibility_type=8, (def)restraint_stdev=(0.0, 1.0), (def)restraint_stdev2=(0.0, 0.0, 0.0), (def)sheet_h_bonds=7, (def)surftyp=1, (def)restraint_parameters=(3, 1, 3, 3, 4, 2, 0, 0.0, 0.086999999999999994), (def)distance_atoms=('CA', 'CA'), (def)atom_ids=('',), (def)residue_ids='') make_re_417_> Restraint type to be calculated: stereo r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1810 2472 2851 788 Total number of restraints before, now : 0 7921 make_re_422_> Number of previous, current restraints : 0 7921 make_re_423_> Number of previous, current selected restraints: 0 7921 runcmd______> model.randomize_xyz(deviation=3.0) randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1757 1757 1 3.0000 randomi_496_> Amplitude is > 0; randomization is done. runcmd______> model.optimize(optimization_method=1, (def)init_velocities=True, (def)temperature=293.0, (def)md_time_step=4.0, (def)min_atom_shift=0.01, (def)cap_atom_shift=0.20000000000000001, (def)write_all_atoms=True, (def)no_ter=False, (def)trace_output=0, (def)equilibrate=999999, max_iterations=300, (def)residue_span_range=(0, 99999), md_return='FINAL', output='REPORT', (def)id2=1, (def)root_name='undf', (def)file_id='default', (def)file_ext='', (def)output_directory='') pair2___215E> Dynamic memory allocation failed. Routine, variable, status: icat1 Mod8v2 generates the: .ini define_symmetry-1.atm define_symmetry-2.atm .pdb files. When mod8v2 was released I used it but the result does not changed. Where is the trouble? I attached here my new2.py. I'm building a model of a homopentamer with 1055 amino acids, is it too big for the software requirements? Thanks in advance. Giovanni **************************************************** Dr. Giovanni GRAZIOSO Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 - 20131 Milano (Italy) Phone: 02/50317570 Fax: 02/50317565 e-mail: giovanni.grazioso(a)unimi.it Web site: http://users.unimi.it/demicheli/gg1.htm ****************************************************

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SET DEVIATION
by Adam C Marko 02 Mar '06

02 Mar '06

Hello all, I am using modeller 8v1 and trying to build a set of models that all differ from one another. I cannot figure out the equivalent command in 8v1 to the command: 'SET DEVIATION = 4.0 # Amount of randomization between models' in 6v2. Thank you for your help, Adam Adam C. Marko National Resource for Biomedical Supercomputing Pittsburgh Supercomputing Center Pittsburgh, PA 15213 www.psc.edu/~marko

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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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[modeller_usage]molecular modelling with multiple chains
by 典范 01 Mar '06

01 Mar '06

Hello all, Could you please tell me how to perform molecular modelling with multiple chains? I get trouble in preparing the alignment file in this case. The sequence of the template is as follows: ******************************************************************************** TEMPLATE:A|PDBID|CHAIN|SEQUENCE ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK TEMPLATE:B|PDBID|CHAIN|SEQUENCE KRRWKKNFIAVSAANRFKKISSSGAL ******************************************************************************** the residue number of Chanin A:148; Chain B:26 The sequence of the target is as listed: ******************************************************************************** TARGET:A|PDBID|CHAIN|SEQUENCE ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELADMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEKIREAFRVFDKDGNGFISAKELRHVMTNLGEKLKDEEVDEMIREADIDGDGQVNYEEFVTMMTSK TARGET:B|PDBID|CHAIN|SEQUENCE KLRWLKNFIAVSKKNRFLKISSSGAL ******************************************************************************** Both the two chains have the same number of residues compared with Template. I want to model the protein-peptide COMPLEX (NOT one by one) of TARGET:A-TARGET:B taking the TEPLATE as template structure. Could anyone please help me to know how to prepare the allignment file and paste it to me? Best regards, DianFan Li China 2006-03-01 ps: the typical ali file in example of MODELLER 7v7 is: *************************************************************************** P1;5fd1 structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------* ****************************************************************************

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Modeller 8v2 release
by Modeller Caretaker 28 Feb '06

28 Feb '06

The new version of Modeller, 8v2, is now available for download from http://salilab.org/modeller/. If you have a license key for Modeller 8v1 or 7v7, there is no need to reregister for Modeller 8v2 - the same license key will work. (It won't do any harm to reregister if you want to, though!) If you encounter bugs in Modeller 8v2, please see http://salilab.org/modeller/manual/node11.html for information on how to report them. 8v2 is largely a bug fix release for 8v1: no changes to your 8v1 Python scripts are necessary to use 8v2, and TOP scripts (from Modeller 7 or 8) will still work. Fixes include: # Bug fix for model_segment: specifying 'FIRST:@', 'LAST:' will now read in all chains in a multi-chain PDB, even when the first has no ID. # Bug fix: chain breaks were sometimes being placed incorrectly in written-out alignments. # Bug fix: some Python circular references, which were preventing memory from being freed, have been removed, thus fixing some long-running scripts. # Bug fix: pseudo atom tables are now reset where necessary; fixes some 'atom index out of range' errors. # Bug fix: local alignments with alignment.salign() were incorrect in some cases. # Bug fix: alignment.compare_structures() was calculating incorrect RMS values in some cases. # New optimized 2D gap penalties are now used for alignment.salign() by default. # More explanatory error messages for the common 'mismatch between alignment and PDB' problem. # The number of segments for DRMS computation (nsegm) and the matrix offset for structural local alignment (matrix_offset_3d) can now be specified in alignment.salign(). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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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

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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

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