- modeller_usage - salilab.org

Re: [modeller_usage] [ question ] atom files?
by Frederico Arnoldi 21 Jul '06

21 Jul '06

Hi Cathy, Please send your script and I will try to help you. Fred >Message: 2 >Date: Fri, 21 Jul 2006 17:00:09 +0900 >From: "Cathy Chang" <aochang(a)ucsd.edu> >Subject: [modeller_usage] [ question ] atom files? >To: <modeller_usage(a)salilab.org> >Message-ID: <002b01c6ac9b$b0438080$830ba8c0@IBMMUNCHIE> >Content-Type: text/plain; charset="us-ascii" > >Hi, > >My name is Cathy. I'm a new user of Modeller, and I'm still trying to >figure >out the input files to run Modeller. I'm having trouble with the atom >files...I don't exactly know what is an atom file. > >I tried using the .pdb file straight from the PDB. I tried changing the >file >content to just the "atom" section of the PDB files. And nothing seems to >work. > >I have the script file & alignment file in the default Modeller directory, >and I set the atom file environment to a folder named "atom_files" with the >2 atom files (1pme & 1wbn). But when I try running my script, it says that >atom files cannot be found in the directory atom_files. Here's the exact >error message: > >==================== > >Read the alignment from file : 1pme_1wbn.ali >Total number of alignment positions: 388 > > # Code #_Res #_Segm PDB_code Name >---------------------------------------------------------------------------- >--- > 1 1pme 380 1 1pme > 2 1wbn 360 1 1wbn >runcmd______> alignment.check() > >check_a_343_> >> BEGINNING OF COMMAND >openf5__224_> Open 11 OLD SEQUENTIAL >\Modeller8v2\atom_files\1pme.atm >rdpdb___303E> No atoms were read from the specified input PDB file, since >the > starting residue number and/or chain id in MODEL_SEGMENT (or > the alignment file header) was not found; > requested starting position: residue number " 0", chain " " >rdabrk__288W> Protein not accepted: 1 1pme >check_a_337E> Structure not read in (please consult the log file > for more details): 1 1pme > >==================== > >It would be great if anyone can help me with this problem! Thank you very >much for your time! > >- Cathy >

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mutating the model
by Prabhakar. G. 13 Jul '06

13 Jul '06

dear modellers, I am tring to mutate a particular residue in a protein using the below script but getting the error, could someone help, Error Traceback (most recent call last): File "(stdin)", line 93, in ? File "C:\Program Files\Modeller8v2\modlib\modeller\model.py", line 220, in generate_topology io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 197, in generate_topology return _modeller.generate_topology(mdl, aln, io, libs, *args) _modeller.error: gener___479E> Must not use patching residues here. Residue type index, residue type: 35 ------------------------------------------------------------------------------------------------------------------------------------------------------------------ command: mod8v2 - < mutate.py 1qhd 2 GLU A > 1qhd.log ------------------------------------------------------------------------------------------------------------------------------------------------------------------ The script import sys import os # # mutate_model.py # # Usage: mod8v2 - < mutate_model.py modelname respos resname chain > logfile # # Example: mod8v2 - < mutate_model.py 1t29 1699 LEU A > 1t29.log # # # Creates a single in silico point mutation to sidechain type and at residue position # input by the user, in the structure whose file is modelname.pdb # The conformation of the mutant sidechain is optimized by conjugate gradient and # refined using some MD. # def optimize(mdl1): #conjugate gradient for step in range(0,len(mdl1.schedule)): mdl1.schedule.step = step + 1 mdl1.optimize (optimization_method=1,max_iterations=200,min_atom_shift=0.001) #md refine(mdl1) mdl1.optimize(optimization_method=1,max_iterations=200,min_atom_shift= 0.001) #molecular dynamics def refine(mdl1): # at T=1000, max_atom_shift for 4fs is cca 0.15 A. init_vel = True for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)), (200, 600, (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))): for temp in temps: mdl1.optimize(cap_atom_shift=0.39, md_time_step=4.0, optimization_method=3, md_return='FINAL', init_velocities=init_vel, temperature=temp, max_iterations=its, equilibrate=equil) init_vel = False #use homologs and dihedral library for dihedral angle restraints def make_restraints(mdl1, aln): rsr = mdl1.restraints rsr.clear() for typ in ('stereo', 'phi-psi_binormal'): rsr.make(restraint_type=typ, aln=aln, spline_on_site=True) for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'): rsr.make(restraint_type=typ+'_dihedral', spline_range=4.0, spline_dx= 0.3, spline_min_points = 5, aln=aln, spline_on_site=True) #first argument modelname, respos, restyp, chain, = sys.argv[1:] log.verbose() env = environ(rand_seed=-49837) env.io.hetatm = True #soft sphere potential env.edat.dynamic_sphere=False #lennard-jones potential (more accuate) env.edat.dynamic_lennard=True env.edat.contact_shell = 4.0 env.edat.update_dynamic = 0.39 # Read customized topology file with phosphoserines (or standard one) env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read customized CHARMM parameter library with phosphoserines (or standard one) env.libs.parameters.read(file='$(LIB)/par.lib') # Read the original PDB file and copy its sequence to the alignment array: mdl1 = model(env, file=modelname) ali = alignment(env) ali.append_model(mdl1, atom_files=modelname, align_codes=modelname) #set up the mutate residue selection segment mdl1.pick_atoms(pick_atoms_set=1, selection_from ='2', res_types ='GLU', selection_segment = (respos+':'+chain, respos+':'+chain), atom_types = 'ALL', selection_status = 'INITIALIZE') #perform the mutate residue operation mdl1.mutate(residue_type=restyp) #get two copies of the sequence. A modeller trick to get things set up ali.append_model(mdl1, align_codes=modelname) # Generate molecular topology for mutant mdl1.generate_topology(ali, sequence=modelname) # Transfer all the coordinates you can from the template native structure # to the mutant (this works even if the order of atoms in the native PDB # file is not standard): #here we are generating the model by reading the template coordinates mdl1.transfer_xyz(ali) # Build the remaining unknown coordinates mdl1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') #yes model2 is the same file as model1. It's a modeller trick. mdl2 = model(env, file=modelname) #required to do a transfer_res_numb #ali.append_model(mdl2, atom_files=modelname, align_codes=modelname) #transfers from "model 2" to "model 1" mdl1.res_num_from(mdl2,ali) #It is usually necessary to write the mutated sequence out and read it in #before proceeding, because not all sequence related information about MODEL #is changed by this command (e.g., internal coordinates, charges, and atom #types and radii are not updated). mdl1.write(file=modelname+restyp+respos+'.tmp') mdl1.read(file=modelname+restyp+respos+'.tmp') #set up restraints before computing energy #we do this a second time because the model has been written out and read in, #clearing the previously set restraints make_restraints(mdl1, ali) #a non-bonded pair has to have at least as many selected atoms mdl1.env.edat.nonbonded_sel_atoms=1 mdl1.schedule.make(library_schedule=6) #only optimize the selected residue (in first pass, just atoms in selected #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment mdl1.pick_atoms(pick_atoms_set=1, selection_from ='2', res_types ='GLU', selection_segment = (respos+':'+chain, respos+':'+chain), atom_types = 'ALL', selection_status = 'INITIALIZE') mdl1.restraints.unpick_all() mdl1.restraints.pick() mdl1.energy() mdl1.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(mdl1) #feels environment (energy computed on pairs that have at least one member #in the selected) mdl1.env.edat.nonbonded_sel_atoms=1 optimize(mdl1) mdl1.energy() #give a proper name mdl1.write(file=modelname+restyp+respos+'.pdb') #delete the temporary file os.remove(modelname+restyp+respos+'.tmp'); ---------------------------------------------------------------------------------------------------------------------------------------------------------- Thanks in advance prabhakar

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Tyrosinekinase-Modelling
by Torsten Stauder 10 Jul '06

10 Jul '06

Hi mailing list! I'm new to "modeller" and actually my modelling doesn't work. However... let my explain... Given is a tyrosine kinase, whose structure is already known. In some cases, this tyrosine kinase is mutated and a so called "internal tandem duplication" [itd] is inserted. It looks like this: wild type sequence: AAAAAAAAAAAAABBBBBBBBBBBBBBB itd: AAAAAAAAAAAAAxxxxxxxxxxxBBBBBBBBBBBBBBB (x = insertion) So I have been performing an alignment and tried to run it with modeller. "model-default.py" was used for the first test. Here is, what the logfile "says": Kind, OS, HostName, Kernel, Processor: 4, Linux audio 2.6.15.1 i686 Date and time of compilation : 02/28/2006 18:03:39 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/07/10 18:27:11.105 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['a627', '1rjb'], atom_files=[], file='alignment_final.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open alignment_final.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 2270569 2217.353 2.165 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2293501 2239.747 2.187 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2316901 2262.599 2.210 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2363701 2308.302 2.254 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2457301 2399.708 2.343 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2644501 2582.521 2.522 Read the alignment from file : alignment_final.ali Total number of alignment positions: 426 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 a627 426 1 a627 FLT3 mutated ITD 2 1rjb 344 1 1rjb FLT3 wild type runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in (please consult the log file for more details): 1 a627 This is my modified "model-default.py" from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'alignment_final.ali', # alignment filename knowns = 'a627', # codes of the templates sequence = '1rjb') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling Any hints? Why has the structure not read? Another question: Do I have to provide my sequence to be modelled a .pdb-file using "0.00" as coordinates or is it sufficient to provide it as .fasta? Thanks in advance.

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Model assessment - GA341
by Cassiano 08 Jul '06

08 Jul '06

Hi all, I have some questions about the model.asses_ga341. In the manual on-line is described that it uses the "percentage sequence identity between the template and the model as a parameter". But, in the cited work (Melo et al, 2002) i don't see this relation with sequence identity. My questions: - How Modeller treat the sequence identity in the context of the cited work? - If the identity between my target and templates is very low, how the quality of the model is affected? (and what you recommend to use to assess the quality) Thanks, Cassiano Carromeu.

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Metal ions
by Joel Tyndall 06 Jul '06

06 Jul '06

Hi message board, I have been trying to include a zinc atom in my model based on the same ion in the template but I just can't crack it. I have attached all relevant files and log file. I am using mod8v2. Advice is much appreciated Cheers Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 MODELLER 8v2, Feb 28, 2006 05:48pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2006 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux allroy.otago.ac.nz 2.6.9-5.ELsmp x86_64 Date and time of compilation : 02/28/2006 18:38:42 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/07/07 09:55:15.134 rdabrk__290E> Number of residues in the alignment and pdb files are different: 66 65 For alignment entry: 1 2fk4 x (mismatch at alignment position 66) Alignment FHNIRGRWTGRCMSCSRSSRz PDB FHNIRGRWTGRCMSCSRSSR Match ******************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. check_a_337E> Structure not read in (please consult the log file for more details): 1 2fk4 top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2331663 2277.015 2.224 Starting time : 2006/07/07 09:55:15.134 Closing time : 2006/07/07 09:55:16.008 Total CPU time [seconds] : 0.87 INCLUDE SET ALNFILE = 'hpv_16_e6_Nterm_2fk4.ali' SET KNOWNS = '2fk4' SET SEQUENCE = 'hpv_16_Nterm_e6' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' SET HETATM_IO = on >P1;2fk4 structureX:2fk4: 3 :A: 68 ::::: SYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSR/z* >P1;hpv_16_Nterm_e6 sequence:hpv_16_Nterm_e6: : : : ::: 0.00: 0.00 PRKLP--QLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYS/z*

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I have problem my protien has some area seems to be extra
by Zartasha Mustansar 03 Jul '06

03 Jul '06

My template is single ... The generated output models (i created 10 moedls with modeller) the model with best energy has some area leaning out of the structure which seems to be not included in the protien ....(When Viewed with Swiss pdb Viewer) How could i made it fit to the alignment with template. i m attaching that output file with it. its a sequence of a Baffalo family (Nili ravi); Thanx! -- Zartasha Mustansar. Sky May be the limit for others ! But it is just The Beginning For Us..! ( ~ Islamians..) -----------------------------(The competitive Bio-Informaticians ! )--------------------------

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modeller
by Patrycja Barbara Lewkowicz 01 Jul '06

01 Jul '06

Hello ! I was trying to make a model in modeller and there's one problem that occured: return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in: 1 Can you help me? It's a new program for me and I acctually have no idea what it wrong. thank you for help Patrycja

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Query
by Madhan Kumar A 30 Jun '06

30 Jun '06

Sir(s), I had written to you yesterday, reporting an error message. As you had suggested, I have attached the alignment file, PDB file, script file and the log file. Kindly let me know what the problem is. Thanking you in advance. Madhan Kumar

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align_2d vs salign
by Mike White 30 Jun '06

30 Jun '06

Hi there, I am modeling a homopentamer using three structures of homologous homopentamers as the template.The monomers are 210 aa's. Following the advanced tutorial, I first aligned the three known structures using salign with the three cycles of refinement, and got good alignment. In the tutorial, the next step was to then align the test sequence with the aligned templates using align_2d. After approximately 3900 seconds this produced what looks like a nice alignment, with structural features such as cys involved in disulfides and conserved aromatic residues lining up between all four sequences (three templates, one test). I then did the alignment using salign instead of align_2d, following the description in the online manual for salign (examples/salign.saling_align_2d). Once again, a nice (but slightly different in the regions without much homology, but still with the other features retained) is obtained. The surprising thing is that this alignment only took 17 seconds, a 200-fold improvement in time). Both alignments gave acceptable-looking models. Are the two algorithms so different that salign is that much faster? Is there any advantage to using align_2d instead of salign? Thanks Mike White Here are the two scripts: ************************************************************************** ALIGN-2D: # Demonstrating ALIGN2D, aligning with variable gap penalty # uses a version of the 5HT3ARXD with first 12 residues removed (no overlap with templates) # default gap_penalties_2d: (3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.) # default gap_penalties_1d: (-450, -50) from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned structure(s): aln = alignment(env) aln.append(file='achbpsPentamer.ali', align_codes='all') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='5HT3ARXDPentamerTrim.ali', align_codes='5HT3ARXDPentamerTrim') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.align2d(overhang=0, gap_penalties_1d=(-450, -50), gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.), align_block=aln_block) # write files. In *.pap files indicate helices and beta structures aln.write(file='5HT3ARXDPentamerTrim-mult.ali', alignment_format='PIR') aln.write(file='5HT3ARXDPentamerTrim-mult.pap', alignment_format='PAP', alignment_features=' INDICES HELIX BETA') **************************************************************************** SALIGN: # Demonstrating ALIGN2D using salign commands, aligning with variable gap penalty # uses a version of the 5HT3ARXD with first 12 residues removed (no overlap with templates) # default gap_penalties_2d: (3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.) # default gap_penalties_1d: (-450, -50) from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned structure(s): aln = alignment(env) aln.append(file='achbpsPentamer.ali', align_codes='all') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='5HT3ARXDPentamerTrim.ali', align_codes='5HT3ARXDPentamerTrim') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(rr_file='$(LIB)/as1.sim.mat', output='', max_gap_length=20, gap_function=True, feature_weights=(1.,0., 0., 0., 0., 0.), gap_penalties_1d=(-450,-50), gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.), similarity_flag=True, align_block=aln_block) # write files. In *.pap files indicate helices and beta structures aln.write(file='5HT3ARXDPentamerTrim-multSalign.ali', alignment_format='PIR') aln.write(file='5HT3ARXDPentamerTrim-multSalign.pap', alignment_format='PAP', alignment_features=' INDICES HELIX BETA') *****************************************************************************

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How Modeller avoid CA clashes?
by Yun He 30 Jun '06

30 Jun '06

When the distance between two adjacent CA atoms (i.e. Ca_i and Ca_i+1) is shorter than 3.6 Angstrom, the two residues may take part in clashes. These are severely unrealistic geometry, however, cis-proline may be an exception usually. When we use Modeller to build model, the default model routine (automodel class) seems only to check the improper chain breaks (the distance between two adjacent CA atoms is larger than 8 Angstrom) of templates, but not check the CA clashes of generated models. And the models sometimes have the CA clashes problem. How could Modeller avoid such improper geometry? Add some distance restraints by hand? A typical example: T0345, a target just released of CASP7. Two templates with very high similarities (id% > 65%) are found, 2F8A and 1GP1. Here is my alignment file of 1GP1_A and T0345 -------------- >P1;1GP1A structure:1gp1:10:A:192:A:GLUTATHIONE PEROXIDASE:NA:2.00:0.171 ---RTVYAFSARPLAGGEPFNLSSLRGKVLLIENVASL-GTTVRDYTQMNDLQRRLGPRGLVV LGFPCNQFGHQENAKNEEILNCLKYVRPGGGFEPNFMLFEKCEVNGEKAHPLFAFLREVLPTP SDDATALMTDPKFITWSPVCRNDVSWNFEKFLVGPDGVPVRRYSRRFLTIDIEPDIETLL-* >P1;T0345 sequence:T0345:1: :185: :T0345: :2.00:-1.00 MIAKSFYDLSAINL-DGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF-PRRLVV LGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYP YDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK* --------------- There are two cis-prolines (PRO:97, PRO:150) in each chain of 1GP1, correspondingly, there are two prolines on the same sites of T0345 (PRO:89, PRO:142), and residues around these prolines are very conserved, so I think the prolines in T0345 should be also cis-proline. After building models from this alignment, I have checked the CA clashes of models, and found that there are two clashes: -- pair distance 88 ARG: === 89 PRO: 2.798 A 141 SER: === 142 PRO: 2.803 A -- However there are NO CA clashes occurred in 1GP1. How do the two clashes happen? Are there some means to avoid these clashes? Best regards, Yun 2006/06/30

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