October 2005 - modeller_usage

constrain template secondary structure in energy minimization/loop building
by Frank Peelman 27 Oct '05

27 Oct '05

-- I'm modellling an Immunoglobulin-type domain. When generating the homology models using automodel, the beta sheet structure in the models seems to be disturbed when compared to the template. This is obviously an error in the model as the besta-sheets are conserved in every related family member. As expected, the problem occurs in the loop building and energy minimization steps, as i do not see the loss of beta-sheet structure when using "a.make("exit=2")". What is the best way to avoid loss of beta-sheet structure, e.g. by tethering, restraining sec. structure ...?

1 0

problem with modelling a non-template helix
by Renée Vancraenenbroeck 25 Oct '05

25 Oct '05

dear modellers, I've come to the problem where I have to elongate a helix but the template is absent, I've tried to restrain it into a helixconformation using the following script wich I found in the archive, however it doesn't seem to make any difference. What am I doing wrong? renée vancraenenbroeck renee.vancraenenbroeck(a)student.kuleuven.ac.be from modeller.automodel import * # Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('133', '139'), spline_on_site=False) # This is as usual: log.verbose() env = environ() a = automodel(env, alnfile='Lrrk2-mult5.ali', knowns=('2aedA','1byuA'), sequence='Lrrk2roc') a.starting_model = 1 a.ending_model = 5 a.make()

2 1

chain
by PARVINI 22 Oct '05

22 Oct '05

Dear friends I want to have chain name and amino acid numbers for tetramer protein in modeller output file. For example A 1 A 2 ------- A 30 B 1 B 2 ------ B 30 Would you please help me? Sincerely yours parvini

1 0

multiple protein conformations
by jf163201＠ohio.edu 20 Oct '05

20 Oct '05

Hi, I have a single sequence and several structures of different conformations of the same protein. I would like to use this information to create a single alignment that incorporates the data from all the conformations. The structures are all of the same protein, so they have the same sequence. Once I have the single alignment, then I can use this alignment to create a model for each conformation. Also note that because of the different conformations, the alignment of the sequence with structure A is not (necessarily) the same alignment given if I align the sequence with structue B. My main approach has been to append the structures and the sequence to alignment and then run align2d(). The problem I have here is that because all the structures have the same sequence, the returned alignment just has all the protein sequences aligned with no gaps and my single sequence is just added with all the extra residues overhanging(the sequence is a little longer that the protein sequences) the alignment of the proteins. Is there some way to add a weight to the protein sequences so that they don't overpower the single sequence? Since the protein sequences align perfectly, the addition of the single sequence is negligible to the overall alignent. I thought this was what the align_what='BLOCK' argument was supposed to do, but I didn't have any luck with that either--I tried to put the proteins in one block, and the sequence in another. I've also been trying salign() without success. I'm new to Modeller and this problem seems sufficiently different from the tutorials and examples in the manual to leave me at a loss. Would someone give me some guidance about how to approach this? Thank you, Jim Fonseca

1 0

error when trying to set MDT_LIB_FILE and BIN_LIB_FILE
by Daniel Rigden 19 Oct '05

19 Oct '05

Dear all I sometimes need to reconstruct a complete structure from a main chain alone structure derived from dynamic analysis. To do this I have, in the past, used a modified mkhomcsr routine to take main chain constraints from one structure (the main chain alone) and side chain constraints from another (the original crystal structure). In the past this has worked. Now, for some reason, on a different machine but running the same v6.2 of modeller, I get errors. My remodelled routine looks like this --------------------------------------------- SUBROUTINE ROUTINE = 'mkhomcsr' SET MAX_CA-CA_DISTANCE = 30.0 SET MAX_N-O_DISTANCE = 20.0 SET MAX_SC-MC_DISTANCE = 4.5 SET MAX_SC-SC_DISTANCE = 6.0 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS = OFF ### MNCH restraints! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = 'mc_only' SEQUENCE SET MDT_LIB_FILE = '${LIB}/mnch1.mdt' SET BIN_LIB_FILE = '${LIB}/mnch1.bin' MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_RESTRAINTS = ON etc. --------------------------------------------- but MODELLER gives errors of this type --------------------------------------------- getprog_531W> ROUTINE redefined: mkhomcsr assgn___544E> Variable name not recognized: MDT_LIB_FILE Command line: SET MDT_LIB_FILE = '${LIB}/mnch1.mdt' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: BIN_LIB_FILE Command line: SET BIN_LIB_FILE = '${LIB}/mnch1.bin' etc. --------------------------------------------- Can anyone tell me why Modeller isn't recognising these variable names? It's not a general issue - simpler modelling tasks run fine. Many thanks in advance Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.

2 1

PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP
by Troy Wymore 14 Oct '05

14 Oct '05

************************************************** PITTSBURGH SUPERCOMPUTING CENTER NATIONAL RESOURCE FOR BIOMEDICAL SUPERCOMPUTING WORKSHOP This workshop is funded by a grant to the PSC from the NIH National Center for Research Resources. The grant provides tuition, hotel, supercomputing time, and workshop materials for US academic participants. COMPUTATIONAL BIOPHYSICS WORKSHOP Nov. 28 - Dec. 1 Application Deadline: October 24 Primary Instructor: Prof. Klaus Schulten (UIUC) www.psc.edu/biomed/training/workshops/2005/NAMD/index.html The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. For specific details, including an electronic application form, see: www.psc.edu/biomed/training/workshops/2005/NAMD/index.html Please direct any questions about the workshop to Dr. Troy Wymore (wymore(a)psc.edu)

1 0

howto reverse polarity
by Peter C. Lai 13 Oct '05

13 Oct '05

I am using a structure-based alignment, and I want to model a sequence based on a template, but I want to model my sequence with inverted polarity to the template. That is, I want to model starting from the C-term of the template backwards to its N-term. If I invert my sequence in the alignment, the result is structurally sound, but now they are obviously bonded incorrectly. For example, my template is: >P1;1u19 structureX:1u19.stripped:33:A:65:A: rhodopsin: Bovine: 2.20: 0.200 EPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQH* and my sequence is (n)-FVFKIVIVIGILPLLNLVGVVKLI-(coo) but I want the F positioned near the H end and the ile positioned near the glu in the template etc. How would I go about doing this? -- Peter C. Lai Cesium Hyperfine Enterprises http://cowbert.2y.net/

2 1

model-segment.py problem
by Guido Leoni 11 Oct '05

11 Oct '05

Hi I have modeller8.1 on a windows machine. I try to use the model-segment.pyscript but modeller send me always the same error: forrtl: severe (64): input conversion error, unit -5, file Internal Fo ad Image PC Routine Line Source libifcoremd.dll 0025DD7A Unknown Unknown Unknown libifcoremd.dll 0025B010 Unknown Unknown Unknown libifcoremd.dll 002261B8 Unknown Unknown Unknown libifcoremd.dll 00226670 Unknown Unknown Unknown libifcoremd.dll 0027F5F9 Unknown Unknown Unknown mod8v1.exe 00494996 Unknown Unknown Unknown mod8v1.exe 00491E53 Unknown Unknown Unknown mod8v1.exe 00474A41 Unknown Unknown Unknown mod8v1.exe 0042D906 Unknown Unknown Unknown mod8v1.exe 00422ED8 Unknown Unknown Unknown python23.dll 26D0A705 Unknown Unknown Unknown python23.dll 26C99DA7 Unknown Unknown Unknown python23.dll 26CAF9E6 Unknown Unknown Unknown python23.dll 26CAC424 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CE8CF0 Unknown Unknown Unknown python23.dll 26C99DA7 Unknown Unknown Unknown python23.dll 26CAF9E6 Unknown Unknown Unknown python23.dll 26CAC424 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CAF4A9 Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CAF3FD Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CAF3FD Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CAF4A9 Unknown Unknown Unknown python23.dll 26CAF1F9 Unknown Unknown Unknown python23.dll 26CAC250 Unknown Unknown Unknown python23.dll 26CADAAE Unknown Unknown Unknown python23.dll 26CA8922 Unknown Unknown Unknown python23.dll 26D22BD4 Unknown Unknown Unknown python23.dll 26D22B86 Unknown Unknown Unknown python23.dll 26D22B50 Unknown Unknown Unknown python23.dll 26D21B2E Unknown Unknown Unknown python23.dll 26D21569 Unknown Unknown Unknown python23.dll 26D214B4 Unknown Unknown Unknown mod8v1.exe 004086BC Unknown Unknown Unknown mod8v1.exe 00401347 Unknown Unknown Unknown mod8v1.exe 005E8C41 Unknown Unknown Unknown mod8v1.exe 005E679B Unknown Unknown Unknown kernel32.dll 7C816D4F Unknown Unknown Unknown _____________________________________________________________ my script is: from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'select_atoms' routine in the 'automodel' class class mymodel(automodel): def select_atoms(self): self.pick_atoms (selection_segment=('923:','924:','925:','926:','927:','928:','929:','930:','931:','932:','933:','934:','935:','936:','937:','938:','939:','940:','941:','942:','943:','944:','945:','946:','947:','948:','949:','950:','951:','952:','953:','954:','955:','956:','957:','958:','959:','960:','961:','962:','963:','964:','965:','966:','967:','968:','969:','970:','971:','972:','973:','974:','975:','976:','977:','978:','979:','980:','981:','982:','983:','984:','985:','986:','987:','988:','989:','990:'), selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status='initialize') env = environ() # directories for input atom files env.io.atom_files_directory = 'C:\master' # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 a = mymodel(env, alnfile = 'fosfalcapirstrano1daq.ali', # alignment filename knowns = '1DAQB', # codes of the templates sequence = '14521248') # code of the target a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling ----------------------------------------------------------------------------------------------------------------- my alignment file is : >P1;1K7H structure:1K7H :1 :A : :B :unknown:unknown:-1:-1 ---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVIFFLGDGMSLSTVTAARIYKGGLTGK -FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLF TYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDRE--DPE-I--CDDIAEQLVFREPGK NFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLDDKASQGATASYVWNRDDLLAV-DIA NTD----YLMGLFSYTHLDTVL---------------------TRDAEMDPTLPEMTKVAIEMLTKDENGFFLLV EGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHGHTLTITGYA------------DRNT DILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRYASAAPKHSATHDGTDVGIWVNGPFA HLFTGVYEENYIPHALAYAACVGTGRTFCD--------------------------------------------- ------------------------/---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVI FFLGDGMSLSTVTAARIYKGGLTGK-FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKT NQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDR E--DPE-I--CDDIAEQLVFREPGKNFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLD DKASQGATASYVWNRDDLLAV-DIANTD----YLMGLFSYTHLDTVL---------------------TRDAEMD PTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHG HTLTITGYA------------DRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRY ASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEENYIPHALAYAACVGTGRTFCD* >P1;1EW2 structure:1EW2 :1 :A : :B :unknown:unknown:-1:-1 ----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDK LGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTR--GNE VISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP--AS--ARQEG--CQDIATQLISNM--- DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWLAKR----QGARYVWNRTELMQASLDP SVT----HLMGLFEPGDMKYEI---------------------HRDSTLDPSLMEMTEAALRLLSRNPRGFFLFV EGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADHSHVFSFGGYP------------LRGS SIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQA HLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP------------------------------------------ -------------------------/----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNL IIFLGDGMGVSTVTAARILKGQKKDKLGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVK GNFQTIGLSAAARFNQCNTTR--GNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP-- AS--ARQEG--CQDIATQLISNM---DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWL AKR----QGARYVWNRTELMQASLDPSVT----HLMGLFEPGDMKYEI---------------------HRDSTL DPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADH SHVFSFGGYP------------LRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP* >P1;1ED9 structure:1ED9 :1 :A : :B :unknown:unknown:-1:-1 TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAE----- -GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHE------------KD HPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALE-KGGKGSITEQLLN----A RADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQARG------YQLVSDAASLNSV-T-- -EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQV EGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGA VM---------------VMSYGN------------------------------SEEDSQEHTGSQLRIAAYGPHA ANVVGLTDQTDLFYTMKAALGLK---------------------------------------------------- ------------------------/TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNII LLIGDGMGDSEITAARNYAE------GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKT YNGALGVDIHE------------KDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKC PGNALE-KGGKGSITEQLLN----ARADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQA RG------YQLVSDAASLNSV-T---EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSV PTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA HASQIVAPDTKAPGLTQALNTKDGAVM---------------VMSYGN--------------------------- ---SEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK* >P1;1DAQA structure:1DAQA :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISIN TDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG-------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------* >P1;1DAQB structure:1DAQB :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------/--------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------------------MSTKLYGDVND DGKVNSTDAVALKRYVLRSGISINTDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG* >P1;14521248 sequence:14521248:1 :A : :B :unknown:unknown:-1:-1 ----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNME DFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVKTYNRMISTTNVTGKL---------VN LTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLILHNVT--------------------- ---VLMGGGREKFSEEVLKLAEDYGY---------------------------------SIVYTREDLEKVKDG- -------KVLGLFAEGHLPYVL----------------------DRSEEDVSLLEMTKKAIEILEKNPNGFFLMI EGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDAS IEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLL AYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLLGDLVDTELE NIADMDNNGIIDLLDVMAILQASS/-----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNV IILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVK TYNRMISTTNVTGKL---------VNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLI LHNVT------------------------VLMGGGREKFSEEVLKLAEDYGY----------------------- ----------SIVYTREDLEKVKDG--------KVLGLFAEGHLPYVL----------------------DRSEE DVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADH ETGGLGIGLNYGHSVDIDSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNI IGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS* _________________________________________________________________________________________ someone can help my? thank's in advance

2 1

RE:model-segment.py
by Riadh HAMMAMI 11 Oct '05

11 Oct '05

Hi, The alignment file should contain: structureX for templates and SequenceX for the target. Why started from model 3:starting_model= 3? hope this help, Yours, Riadh HAMMAMI PhD Student University of Tunis El Manar, TUNISIA »»»»» Your script is: from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'select_atoms' routine in the 'automodel' class class mymodel(automodel): def select_atoms(self): self.pick_atoms (selection_segment=('923:','924:','925:','926:','927:','928:','929:','930:','931:','932:','933:','934:','935:','936:','937:','938:','939:','940:','941:','942:','943:','944:','945:','946:','947:','948:','949:','950:','951:','952:','953:','954:','955:','956:','957:','958:','959:','960:','961:','962:','963:','964:','965:','966:','967:','968:','969:','970:','971:','972:','973:','974:','975:','976:','977:','978:','979:','980:','981:','982:','983:','984:','985:','986:','987:','988:','989:','990:'), selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status='initialize') env = environ() # directories for input atom files env.io.atom_files_directory = 'C:\master' # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 a = mymodel(env, alnfile = 'fosfalcapirstrano1daq.ali', # alignment filename knowns = '1DAQB', # codes of the templates sequence = '14521248') # code of the target a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling ----------------------------------------------------------------------------------------------------------------- Your alignment file should be : >P1;1K7H structurex:1K7H :1 :A : :B :unknown:unknown:-1:-1 ---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVIFFLGDGMSLSTVTAARIYKGGLTGK -FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLF TYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDRE--DPE-I--CDDIAEQLVFREPGK NFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLDDKASQGATASYVWNRDDLLAV-DIA NTD----YLMGLFSYTHLDTVL---------------------TRDAEMDPTLPEMTKVAIEMLTKDENGFFLLV EGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHGHTLTITGYA------------DRNT DILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRYASAAPKHSATHDGTDVGIWVNGPFA HLFTGVYEENYIPHALAYAACVGTGRTFCD--------------------------------------------- ------------------------/---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVI FFLGDGMSLSTVTAARIYKGGLTGK-FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKT NQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDR E--DPE-I--CDDIAEQLVFREPGKNFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLD DKASQGATASYVWNRDDLLAV-DIANTD----YLMGLFSYTHLDTVL---------------------TRDAEMD PTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHG HTLTITGYA------------DRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRY ASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEENYIPHALAYAACVGTGRTFCD* >P1;1EW2 structurex:1EW2 :1 :A : :B :unknown:unknown:-1:-1 ----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDK LGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTR--GNE VISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP--AS--ARQEG--CQDIATQLISNM--- DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWLAKR----QGARYVWNRTELMQASLDP SVT----HLMGLFEPGDMKYEI---------------------HRDSTLDPSLMEMTEAALRLLSRNPRGFFLFV EGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADHSHVFSFGGYP------------LRGS SIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQA HLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP------------------------------------------ -------------------------/----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNL IIFLGDGMGVSTVTAARILKGQKKDKLGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVK GNFQTIGLSAAARFNQCNTTR--GNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP-- AS--ARQEG--CQDIATQLISNM---DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWL AKR----QGARYVWNRTELMQASLDPSVT----HLMGLFEPGDMKYEI---------------------HRDSTL DPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADH SHVFSFGGYP------------LRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP* >P1;1ED9 structure:1ED9 :1 :A : :B :unknown:unknown:-1:-1 TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAE----- -GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHE------------KD HPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALE-KGGKGSITEQLLN----A RADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQARG------YQLVSDAASLNSV-T-- -EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQV EGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGA VM---------------VMSYGN------------------------------SEEDSQEHTGSQLRIAAYGPHA ANVVGLTDQTDLFYTMKAALGLK---------------------------------------------------- ------------------------/TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNII LLIGDGMGDSEITAARNYAE------GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKT YNGALGVDIHE------------KDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKC PGNALE-KGGKGSITEQLLN----ARADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQA RG------YQLVSDAASLNSV-T---EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSV PTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA HASQIVAPDTKAPGLTQALNTKDGAVM---------------VMSYGN--------------------------- ---SEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK* >P1;1DAQA structurex:1DAQA :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISIN TDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG-------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------* >P1;1DAQB structurex:1DAQB :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------/--------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------------------MSTKLYGDVND DGKVNSTDAVALKRYVLRSGISINTDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG* >P1;14521248 sequenceX:14521248:1 :A : :B :unknown:unknown:-1:-1 ----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNME DFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVKTYNRMISTTNVTGKL---------VN LTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLILHNVT--------------------- ---VLMGGGREKFSEEVLKLAEDYGY---------------------------------SIVYTREDLEKVKDG- -------KVLGLFAEGHLPYVL----------------------DRSEEDVSLLEMTKKAIEILEKNPNGFFLMI EGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDAS IEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLL AYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLLGDLVDTELE NIADMDNNGIIDLLDVMAILQASS/-----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNV IILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVK TYNRMISTTNVTGKL---------VNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLI LHNVT------------------------VLMGGGREKFSEEVLKLAEDYGY----------------------- ----------SIVYTREDLEKVKDG--------KVLGLFAEGHLPYVL----------------------DRSEE DVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADH ETGGLGIGLNYGHSVDIDSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNI IGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS* _________________________________________________________________________________________

1 0

(sans objet)
by Riadh HAMMAMI 11 Oct '05

11 Oct '05

Hi, The alignment file should contain: structureX for templates and SequenceX for the target. Why started from model 3:starting_model= 3? hope this help, Yours, Riadh HAMMAMI PhD Student University of Tunis El Manar, TUNISIA »»»»» Your script is: from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'select_atoms' routine in the 'automodel' class class mymodel(automodel): def select_atoms(self): self.pick_atoms (selection_segment=('923:','924:','925:','926:','927:','928:','929:','930:','931:','932:','933:','934:','935:','936:','937:','938:','939:','940:','941:','942:','943:','944:','945:','946:','947:','948:','949:','950:','951:','952:','953:','954:','955:','956:','957:','958:','959:','960:','961:','962:','963:','964:','965:','966:','967:','968:','969:','970:','971:','972:','973:','974:','975:','976:','977:','978:','979:','980:','981:','982:','983:','984:','985:','986:','987:','988:','989:','990:'), selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status='initialize') env = environ() # directories for input atom files env.io.atom_files_directory = 'C:\master' # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 a = mymodel(env, alnfile = 'fosfalcapirstrano1daq.ali', # alignment filename knowns = '1DAQB', # codes of the templates sequence = '14521248') # code of the target a.starting_model= 3 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling ----------------------------------------------------------------------------------------------------------------- Your alignment file should be : >P1;1K7H structurex:1K7H :1 :A : :B :unknown:unknown:-1:-1 ---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVIFFLGDGMSLSTVTAARIYKGGLTGK -FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKTNQGVIGLDANTVRTNCSYQLDESLF TYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDRE--DPE-I--CDDIAEQLVFREPGK NFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLDDKASQGATASYVWNRDDLLAV-DIA NTD----YLMGLFSYTHLDTVL---------------------TRDAEMDPTLPEMTKVAIEMLTKDENGFFLLV EGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHGHTLTITGYA------------DRNT DILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRYASAAPKHSATHDGTDVGIWVNGPFA HLFTGVYEENYIPHALAYAACVGTGRTFCD--------------------------------------------- ------------------------/---------------EEDKAYWNKDAQDALDKQLGI---KLREKQAKNVI FFLGDGMSLSTVTAARIYKGGLTGK-FEREKI-SWEEFDFAALSKTYNTD------KQVTDSAASATAYLTGVKT NQGVIGLDANTVRTNCSYQLDESLFTYSIAHWFQEAGRSTGVVTSTRVTHATPAGTYAHVADRDWENDSDVVHDR E--DPE-I--CDDIAEQLVFREPGKNFKVIMGGGRRGFFPEEALDIEDG----IPGERED-----GKHLITDWLD DKASQGATASYVWNRDDLLAV-DIANTD----YLMGLFSYTHLDTVL---------------------TRDAEMD PTLPEMTKVAIEMLTKDENGFFLLVEGGRIDHMHHANQIRQSLAETLDMEEAVSMALSMT-DPEETIILVTADHG HTLTITGYA------------DRNTDILDFAGISDLDDRRYTILDYGSGPGYHITEDGKRYEPTEEDLKDINFRY ASAAPKHSATHDGTDVGIWVNGPFAHLFTGVYEENYIPHALAYAACVGTGRTFCD* >P1;1EW2 structurex:1EW2 :1 :A : :B :unknown:unknown:-1:-1 ----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDK LGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTR--GNE VISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP--AS--ARQEG--CQDIATQLISNM--- DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWLAKR----QGARYVWNRTELMQASLDP SVT----HLMGLFEPGDMKYEI---------------------HRDSTLDPSLMEMTEAALRLLSRNPRGFFLFV EGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADHSHVFSFGGYP------------LRGS SIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQA HLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP------------------------------------------ -------------------------/----------IIPVEEENPDFWNREAAEALGAAKKL---QPAQTAAKNL IIFLGDGMGVSTVTAARILKGQKKDKLGPEIPL-AMDRFPYVALSKTYNVD------KHVPDSGATATAYLCGVK GNFQTIGLSAAARFNQCNTTR--GNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVP-- AS--ARQEG--CQDIATQLISNM---DIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLD-----GKNLVQEWL AKR----QGARYVWNRTELMQASLDPSVT----HLMGLFEPGDMKYEI---------------------HRDSTL DPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLT-SEEDTLSLVTADH SHVFSFGGYP------------LRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLK-DGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP* >P1;1ED9 structure:1ED9 :1 :A : :B :unknown:unknown:-1:-1 TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAE----- -GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHE------------KD HPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALE-KGGKGSITEQLLN----A RADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQARG------YQLVSDAASLNSV-T-- -EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQV EGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGA VM---------------VMSYGN------------------------------SEEDSQEHTGSQLRIAAYGPHA ANVVGLTDQTDLFYTMKAALGLK---------------------------------------------------- ------------------------/TPEMPVLENRAAQGDITAPGGA--RRLTGD--QTAALRDSLSDKPAKNII LLIGDGMGDSEITAARNYAE------GAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKT YNGALGVDIHE------------KDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKC PGNALE-KGGKGSITEQLLN----ARADVTLGGGAKTFA-----------------ETATAGEWQGKTLREQAQA RG------YQLVSDAASLNSV-T---EANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSV PTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHA HASQIVAPDTKAPGLTQALNTKDGAVM---------------VMSYGN--------------------------- ---SEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK* >P1;1DAQA structurex:1DAQA :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISIN TDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG-------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------* >P1;1DAQB structurex:1DAQB :1 :A :57 : :unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------/--------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------------------------------------------------------MSTKLYGDVND DGKVNSTDAVALKRYVLRSGISINTDN-ADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG* >P1;14521248 sequenceX:14521248:1 :A : :B :unknown:unknown:-1:-1 ----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNME DFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVKTYNRMISTTNVTGKL---------VN LTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLILHNVT--------------------- ---VLMGGGREKFSEEVLKLAEDYGY---------------------------------SIVYTREDLEKVKDG- -------KVLGLFAEGHLPYVL----------------------DRSEEDVSLLEMTKKAIEILEKNPNGFFLMI EGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDAS IEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVSHKHTGEPVPLL AYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTGDYRVDERDAYATLMLLLGDLVDTELE NIADMDNNGIIDLLDVMAILQASS/-----------------MMKMKLARFLLIFIIFSSMFPFANASPSGVRNV IILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLS-----------------GEVTDSAAAGTAIATGVK TYNRMISTTNVTGKL---------VNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPDRDMEEEIARQLI LHNVT------------------------VLMGGGREKFSEEVLKLAEDYGY----------------------- ----------SIVYTREDLEKVKDG--------KVLGLFAEGHLPYVL----------------------DRSEE DVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVAETKEFDDVVGYVLDYARRRGDTLVIVLADH ETGGLGIGLNYGHSVDIDSIRRIDASIEEMSKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNI IGEIISKKLGVGFVSHKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS* _________________________________________________________________________________________

1 0