- modeller_usage - salilab.org

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.

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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)

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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/

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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

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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

(sans objet)
by Riadh HAMMAMI 10 Oct '05

10 Oct '05

Hi, >Running Modeller8v1 I am getting the following error message: >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 Does anyone have a suggestion why it is happening !? You should take about DOS extensions: rename your file for example (adsl_B99990001.pdb), it should be only one ".pdb" extension. Also make attention for the subdirectory you put the PDB file, env.io.atom_files_directory = './:../atom_files/' Hope this help, Riadh HAMMAMI UNIVERSITY OF TUNIS EL MANAR, TUNISIA

3 3

File not found
by Ricardo Nicoluci 10 Oct '05

10 Oct '05

Hi, Running Modeller8v1 I am getting the following error message: 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 Does anyone have a suggestion why it is happening !? Thanks in advance, -- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil

1 0

how to create .ali file
by sankari thirumal 10 Oct '05

10 Oct '05

Dear all, Psiblast search could find a template for my protein sequence with low identity (19%). So i preferred mgenTHREADER. I got the alignment results form genthreader. Now i don't know how to create the .ali file i have a aligned text file and .aln file. Now what is command for creating the .ali file and what are the files i need to make changes in the files (scripts) with my own target sequence. But the psiblast hit and the mgentreader results are not the same. Can I trust the mgenthreader results.? thanks in advance sankari --------------------------------- Yahoo! Music Unlimited - Access over 1 million songs. Try it free.

1 0

Re: plotting with GNU
by Prabhakar. G. 07 Oct '05

07 Oct '05

Hi, I am new user to the modeler, I have started with the basic tutorial, I have difficulty with plotting the dope scores with GNU plot, when I plot the two dat files '1bdma_dope.dat','TVLDH_dope.dat'(from the tutorials folder) I get the graph plotted(Dope score vs Residue Index), but the two graphs are not aligned, as shown in the tutorial html file. how to align the graphs. hope someone could help me with this silly doubt. prabhakar

1 0