July 2006 - modeller_usage

handling missing residues in pdb files when doing multiple alignments
by Mike White 31 Jul '06

31 Jul '06

I am modeling a homopentamer in several different conformations using multiple templates as described in the Advanced tutorial. My modelling process involves using three different templates from homologous proteins and getting a structure-based alignment of the templates using salign. One of the templates has several gaps in the same position in each of the subunits (missing 1-3 amino acids in the structure).The resulting structure-based alignment doesn't show the missing residues as gaps of the proper length (this may be because the missing residues are in the middle of long loop without structure at subunit-subunit interfaces and one might be able to do without one or two residues here). I know that when one uses a single template with missing residues one should correct the alignment between the sequence to be modeled and the template by introducing gaps in the alignment for the missing residues. At what point would one deal with this when using multiple templates? If you insert the gaps in the structure-based alignment before aligning the sequence, are the gaps preserved, or do you then have to tweak the final alignment a bit more before modeling? I assume that the "adjustments are made in the Thanks Mike White

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I don't know how to get the file pdb_95.pir in my case, plz, tell me what to do.
by Ngo Duc Tri 31 Jul '06

31 Jul '06

Dear all, I'm newbie in Modeller so I practice the Tutorial (Basic Example 1). It's ok but when I model my protein, I don't know how we can obtain the file pdb_95.pir which contains sequences that are 95% identity to my protein? Which program or which command will I need to do? Can anyone help me? Thank you very much. With my best regards, TriNgo

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Error in "Unknown residue type, position, sequence" once more.
by Ngo Duc Tri 31 Jul '06

31 Jul '06

I'm sorry to disturb you but i got the old error say that: "read_al_375E> Unknown residue type,position,sequence" when I run the script: model-single.py. I also check the name very careful. It's right. Please tell me how to solve this error. Here is my code: File model-single.py: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='blbp-1ehyA.ali', knowns='1ehyA', sequence='blbp') a.starting_model = 1 a.ending_model = 5 a.make() File blbp-1ehyA.ali: >P1;1ehyA structureX:1ehyA: 2 :A: 294 :A::: 2.10:-1.00 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLND LSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFESWYSQFHQLDMAV EVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLP VTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR* >P1;blbp sequence:blbp::::::: 0.00: 0.00 MPDPASGIAI NRVPANGLEF EVAMAGEGDH LALMLHGFPE LHFSWRHQMP LLAEMGYRVW APNMRGYGET TRPTEVRDYA LDHLTQDVAA LIDASGATKV TLIAHDWGAI IAWYFAILKL RPLERLVIMN VPHPKVLQRE LRRWEQIKKS WYVFFFQLPW LPEKRIGADS GKRIGELFAQ TSCNPERFGP DVKAVYAAGA ARPGAPRAMV NYYRAAMRHR DTIDPGDFRV DVPTLLVWGE EDVALNIRCT EGTEQWVPDI TVKRLPNVSH WVQQDAPDEV NAILREWLPK PAPAS* Thank you very much!!! NgoDucTri

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[ help ] exceeded maxmol_pdf?
by Cathy Chang 26 Jul '06

26 Jul '06

Hi, I'm trying to model a protein that is about 890 aa long. I was provided with 1NW1 to model against; however, the problem I ran into was that the output structure from Modeller had a protein core and a long tail region. I ran my target in 123D+ and found 1JQI to align fairly well with this trailing tail region, so I want to model my target with both 1NW1 (core region - 32:A:426:A) and 1JQI (trailing tail region - 4:A:387:A). However, when I run Modeller, I get all of the output except the PDB file, and this error message keeps appearing in my log file: >> Summary of failed models: acad10.B99990001.pdb Obj. func. (164592.781) exceeded max_molpdf (100000.000) ==> (note: the obj. func. value changes but it's always over the max) I tried changing the domains of both 1NW1 and 1JQI, but I still get the same error message. How would I be able to avoid exceeding the max pdf size if I want to model my target with both of the listed proteins against the specific areas of my target? Thank you for your help! - Cathy

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[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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