September 2005 - modeller_usage

Fwd: [modeller_usage] Python Modeller Script
by Ricardo Nicoluci 30 Sep '05

30 Sep '05

Hi, I thought that the script was woriking well but after running a while the modeller gives the following error: IOError: openf5__225E> File does not exist: file-not-found pdbnam__217W> Filename for PDB code not found: adsl.B99990001.pdb Directories: ./ Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found I checked the variable env.io.atom_files_directory and it is set to './' ...what am I doing wrong !? Any ideia !? Thanks, On 9/27/05, Modeller Caretaker <modeller-care(a)salilab.org> wrote: > > Ricardo Nicoluci wrote: > > Sorry, I really forgot to attach the script file. > > I was trying to put generate.transfer_xyz between quotations marks. > > > > Now, if someone could comment the script, I would appreciate... > > You call a.make() twice, so you'll build all your models twice, which is > inefficient. Get rid of the first a.make() call. > > a.loop.md_level is the same as a.md_level - i.e. you should remove the > quotes from ' refine.very_slow'. > > You don't need to pass topology_model, parlib, or toplib in the > loopmodel() constructor, since these are the defaults. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > -- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil

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symmetry in automodel
by Gordon Wells 27 Sep '05

27 Sep '05

Hi all Is it possible to impose symmetry restraints in automodel? I've tried the following: 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)) segsize = 330 class symmodel(automodel): def special_restraints(self, aln): defsym(self,aln,seg1=('1',str(segsize)), seg2=(str(segsize+1),str(2*segsize))) defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)), seg2=(str(2*segsize+1),str(3*segsize))) The commands are accepted, but have no effect on the final model. -- "FABRICATI DIEM, PVNC" -- Terry Pratchett, Guards! Guards! Gordon Wells Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria

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Python Modeller Script
by Ricardo Nicoluci 27 Sep '05

27 Sep '05

Hi, We used to have a script for modeller in the old type way. Now we translated it to python mode, but the function automodel.generate_method and automodel.rand_method are not working properly. The following error occurs: when a.generate_method is activated: Traceback (most recent call last): File "mod.py", line 75, in ? a.make() # do the actual homology modelling File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 28, in make automodel.make(self, exit_stage) File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 334, in homcsr self.generate_method(self, aln) TypeError: 'str' object is not callable when a.rand_method is activated: File "mod.py", line 75, in ? a.make() # do the actual homology modelling File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 28, in make automodel.make(self, exit_stage) File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 110, in make self.multiple_models() File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 32, in multiple_models automodel.multiple_models(self) File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 197, in multiple_models self.single_model(num) File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 210, in single_model self.rand_method(self) TypeError: 'str' object is not callable Also I would like suggestions to the script file that is attached. Thanks, -- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil

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Question
by asif.iqbal＠iccs.edu 27 Sep '05

27 Sep '05

Dear prof. Andraj Sali i have make a model of four similar chains ic homotetramer each having 250 residues each. but when i model the structure it always conected and model form consisted of one chain ic four chain conected with each other. so how we can make model separate chain in one model AsifIqbal HEJ research intitute of chemistry university of Karachi Pkaitan

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Problems with mod8v1
by Elza Helena Andrade Barbosa 26 Sep '05

26 Sep '05

Hi all, I made a theoretical model in modeller7v7 and now, when I try to do it again in modeller8v1, I get the following error: Traceback (most recent call last): File "<string>", line 1, in ? File "/usr/lib/modeller8v1/modlib/modeller/runtop.py", line 79, in run self.runlines(self.lines) File "/usr/lib/modeller8v1/modlib/modeller/runtop.py", line 131, in runlines indxca = self.run_top_cmd(cmd, indxca, lines, callstack, subrout) File "/usr/lib/modeller8v1/modlib/modeller/runtop.py", line 364, in run_top_cmd self.make_top_variable(0) File "/usr/lib/modeller8v1/modlib/modeller/runtop.py", line 525, in make_top_variable var = var.lower() AttributeError: 'int' object has no attribute 'lower' What does it mean? What have changed in runtop that it can not "understand" my files anymore? Thanks in advance, Elza

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Hi
by zhurx 26 Sep '05

26 Sep '05

Dear Prof. or Dr. After installation(modeller v8.1),I use this command:mod8v1 __spline.top(or other .top files),I get answer:mod8v1[43]:ulimit:exceeds allowable limit. I think the installation of modeller is easier than other softwares,however,I failed. So,I'm very expecting your reply. 　　　　　　　　zhurx(a)mail.sioc.ac.cn 　　　　　　　　　　2005-09-26

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Hi
by zhurx 26 Sep '05

26 Sep '05

Dear Prof. or Dr. Could anyone tell me whether modeller in InsightII can do a whole homology modelling without additional installation of modeller? 　　　　　　　　zhurx(a)mail.sioc.ac.cn 　　　　　　　　　　2005-09-26

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Converting (old) top script to (new) python ones
by Eric Hajjar 23 Sep '05

23 Sep '05

Hi , i've been using Modeller old versions with the old formet --> TOP. The new "polished - python" interface looks really promising , but i'm spending now some time to see how to make things work ! I went throught all tutorials , and that is OK , but in my present case i want to add DISULFIDE RESTRAINTS and i want to change the default "coordinate-output-names" so if i understand right i have to NOT use the "automodel" class anymore... Here starts the trouble ! Also: Before i was doing : SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '27' '50' RETURN END_SUBROUTINE now , according to the manual : "mdl.patch_ss_templates(aln) # Create the stereochemical restraints mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) " If i follow those examples in the manual and try to read my alignement to write the correponding model-with patches constraints. i get a completely unfolded, linear protein as a result ! Here's my input : seq="Criquet" # my sequence align="Criquet-1pce-modifiedbyhand.ali" # my alignement #align="Criquet-1pce.ali" struct="1pceA" #struct2="3ovo" # Read the sequence, calculate its topology, and coordinates: aln = alignment(env, file=align, align_codes=(struct)) # Superpose the two template structures without changing the alignment. # This is for TRANSFER_XYZ to work properly. It relies on not reading # the atom files again before TRANSFER_XYZ. aln.malign3d(fit=False) # This is for TRANSFER_XYZ to work properly. # Restore the alignment, and add in the model sequence, 1fas: aln.append(file=align, align_codes=(struct, seq)) mdl = model(env) mdl.generate_topology(aln, sequence='Criquet') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=True, build_method='INTERNAL_COORDINATES') mdl.write(file=align+'.noSS') # Create the disulfide bonds using equivalent disulfide bonds in templates: mdl.patch_ss_templates(aln) # Create the stereochemical restraints mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) # Calculate energy to test the disulfide restraints (bonds, angles, dihedrals): mdl.energy() Then i got confused: why i'm not able to reproduce a "simple" top script : read an alignement --> build a model ! with the model() class Thanks in advance for looking at this -- ----------------------------- Eric Hajjar Phd Student in Molecular Modeling University of Bergen , Computational Biology Unit BCCS/UNIFOB, Bergen, NORWAY eric.hajjar(a)bccs.uib.no tel:(+47)55584029 mob:(+47) 98023282

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Repeating basic tutorial with my protein - stuck at malign3d step
by Charlotte Habegger-Polomat 22 Sep '05

22 Sep '05

Hello! I have redone the basic tutorial successfully with the example given, and would now like to reproduce those same steps with my protein of interest. In my working directory, I have the PDB files for the structures I'm trying to align and the following compare.py file: ------------------------------------------------ env = environ() aln = alignment(env, file='$(LIB)/CHAINS_all.seq', align_codes=('1n75', '1n77')) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table() env.dendrogram() --------------------------------------------------- I was not sure what $(LIB)/CHAINS_all.seq referred to. If I need to change that line: aln = alignment(env, file='$(LIB)/CHAINS_all.seq', Then what type of file should I use? This is the error message I am getting: ----------------------------------------------------- File "compare.py", line 3, in ? align_codes=('1n75', '1n77')) File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py", line 19, in __init__ self.__int_append('alignment.append', io, libs, vars) File "/usr/local/packages/modeller8v1/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/local/packages/modeller8v1/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1n75 ---------------------------------------------------- and my compare.log: ------------------------------------------------- Kind, OS, HostName, Kernel, Processor: 4, Linux pelican 2.6.7-gentoo-r11 i686 Date and time of compilation : 06/20/2005 12:04:54 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/09/16 11:37:06.955 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1n75 --- ----------------------------------------------- Thank you for any suggestions as to how I can compare the structures! -Charlotte

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problem in modelling
by rathankar rao 22 Sep '05

22 Sep '05

hi all am having a problem in modelling a protein, plz help --------------------------------- Yahoo! for Good Click here to donate to the Hurricane Katrina relief effort. HI ALL Iam modelling a protein in which iam encountering the errors as shown in the below log file. i have tried all hte possible things, but couldnt get the output. i have checked even the pdb files for the residues numbering and if any missing residues are present. but still couldnt model it. plz help. TOP_________> 116 756 CALL ROUTINE = 'model' TOP_________> 117 419 CALL ROUTINE = 'getnames' TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 120 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 121 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 122 538 SET ROOT_NAME = SEQUENCE TOP_________> 123 539 RETURN TOP_________> 124 420 CALL ROUTINE = 'homcsr' TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 145831 142.413 0.139 openf5__224_> Open 20 OLD SEQUENTIAL alignm.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 8701803 8497.854 8.299 openf5__224_> Open 20 OLD SEQUENTIAL alignm.ali Read the alignment from file : alignm.ali Total number of alignment positions: 357 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2PIA 157 1 2PIA Oxido 2 1GVH 50 1 1GVH oxido 3 1TVC 64 1 1TVC oxidored 4 1TXC 34 1 1TXC oxidored 5 1KRH 43 1 1KRH Oxidored 6 1QGA 38 1 1QGA oxidored 7 1H42 45 1 1H42 ZNFING 8 1FNC 48 1 1FNC ZNFING 9 2PDA 92 1 2PDA Oxido 10 1RFK 88 1 1RFK ZNFING 11 reduct 350 1 reduct TOP_________> 126 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 127 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./\2PIA.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1GVH.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1TVC.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1TXC.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1KRH.pdb rdabrk__290E> Number of residues in the alignment and pdb files are different: 43 33 For alignment entry: 5 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 8703453 8499.466 8.300 Starting time : 2005/09/22 15:44:22.046 Closing time : 2005/09/22 15:44:23.250 Total CPU time [seconds] : 1.20 >P1;2PIA StructureX:2PIA :8: :164: :Oxido:HUM: : FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1GVH StructureX:1GVH :212: A :261:A :oxido:uk2: : ------------------------------------------------------------P D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TVC StructureX:1TVC :45:A:108:A :oxidored:uk3: : ---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TXC StructureX:1TXC :216:A:249:A :oxidored:uk3: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF FEKF---LPSG-------------------------------------------------- ------------------------------------------------------* >P1;1KRH StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------* >P1;1QGA StructureX:1QGA :194:A :231:A :oxidored:uk6: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE Q------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------* >P1;1H42 StructureX:1H42 :190:A :235:A :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE QKNPQ--GGR--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1FNC StructureX:1FNC :234: :281: :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------SRE QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI--------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;2PDA StructureX:2PDA :229: :320: :Oxido:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD* >P1;1RFK StructureX:1RFK :204: B :291:B :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET* >P1;reduct Sequence:reduct:1::350::::: FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD* # A sample TOP file for fully automated comparative modeling INCLUDE # include MODELLER routines SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files SET ALNFILE = 'alignm.ali' # input file w/ templates and target SET KNOWNS = '2PIA' '1GVH' '1TVC' '1TXC' '1KRH' '1QGA' '1H42' '1FNC' '2PDA' '1RFK' # templates' PDB codes SET SEQUENCE = 'reduct' # target code SET STARTING_MODEL = 1 SET ENDING_MODEL = 3 SET HETATM_IO = ON SET OUTPUT_CONTROL = 1 1 1 1 1 CALL ROUTINE = 'model' # get alignment and a model

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