- modeller_usage - salilab.org

[Modeler] Question about this alignment
by Hoffmann 26 Jul '06

26 Jul '06

Hello, I have generated several protein models with modeller, However, for the alignment shown before, I didn't suceed. What am I missing? structureX:1dkr:167:A:316:A:PDB::0.00:0.00 DIVIVSPDHGGVTRARKLADRLKAPIAIIDKRXXXXXXXXXMNIVGNIEGKTAILIDDIIDTA----GTITLAANALVENGAKEVYACCT-HPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLFS* >P1;pep sequence::::::SEQ::0.00:0.00 ------------------------------------AVADKRPRGRPRKHS-VISGQDFIEGGWVGWPEARQLAAALCQRRIP-CSVCLTKAVELGAPTDAFWLDPD-GVHCPLVPLRQRPTQRPVTLVSV------------------------* Thanks, Hoffmann __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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modelling fragments
by Viktor Hornak 25 Jul '06

25 Jul '06

Dear All, I was trying to use Modeller to produce coordinates of parts of a given target sequence based on full PDB coordinates of a template. For example: my template has a sequence AAAAABBCCCCCDDEEEEE which represents three helices (AAAAA, CCCCC, EEEEE) connected by two loops (BB, DD). My target has a sequence aaaaabbcccccddeeeee (again three helices and two loops) and I would like to overlap target helices on the template helices such that the loops in target are ignored. In other words, the resulting coordinates for the target would just have three helices (aaaaa, ccccc, eeeee). I have tried different alignment variants, such as: >P1;mol1 structureX:mol1:1: :19: : :2.2: AAAAABBCCCCCDDEEEEE* >P1;mol2 sequence:mol2: : : : : : : aaaaa--ccccc--eeeee* but the target sequence always wants to be connected; I don't know how to make Modeller to produce three helical fragments modeled on template helices of the full PDB structure. If some Modeller expert could provide advice or point out what I am doing wrong, I would greatly appreciate it... Thanks! -Viktor -- ===================== Viktor Hornak SUNY at Stony Brook =====================

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[ question ] atom files?
by Cathy Chang 21 Jul '06

21 Jul '06

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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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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