- modeller_usage - salilab.org

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* _________________________________________________________________________________________

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(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

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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

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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.

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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

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No optimization
by mathieu coincon 06 Oct '05

06 Oct '05

Hi, I had a structure where a 15-residues loop is missing. So I want to create it but without moving the other atoms. I tried a lot of things (md_level= None, and so...) but I wasn't able to obtain a model where the non-loop atoms stayed in place. I think that there is still an optimization I can't stop. After that I could try to optimize my loop with the refine_loop.py from the advanced tutorial but first I need my model. Can someone help me please? Mathieu Coincon PhD Student Universite de Montreal

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Re: modeller_usage Digest, Vol 4, Issue 90
by Prabhakar. G. 05 Oct '05

05 Oct '05

modeller care taker and users, 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 Project Trainee, Bioinformatics and Data Management, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411 007 Maharastra India On 10/5/05, modeller_usage-request(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: modeling of transmembrane proteins (Modeller Caretaker) > 2. Re: Modelling nucleic acids (nisha(a)ncbs.res.in) > 3. DOPE score (Leyla Celik) > 4. Re: DOPE score (Modeller Caretaker) > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Akansha Saxena <asaxena17(a)yahoo.com> > Date: Tue, 04 Oct 2005 11:02:18 -0700 > Subject: Re: [modeller_usage] modeling of transmembrane proteins > Akansha Saxena wrote: > > I used modeller to build a model for transmembrane > > protein (its an ion channel). The model is fine but > > has variations from the template structure. I wanted > > to know does modeller uses some different constraints > > for a transmembrane protein or it is similar to all > > other proteins. > > Modeller does not do anything special for transmembrane proteins; it > simply extracts restraints from the template structures. Note, however, > that Modeller's internal database of protein alignments, used to derive > statistics, include no transmembrane proteins, so it may not behave as > well as for globular systems. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > > ---------- Forwarded message ---------- > From: nisha(a)ncbs.res.in > To: modeller_usage(a)salilab.org > Date: Wed, 5 Oct 2005 15:40:36 +0530 (IST) > Subject: Re: [modeller_usage] Modelling nucleic acids > Hello Modeller Users > > Charlotte, thank you for your reply. However, I have included the number > of nucleic acid residues in the description line of the structure and > sequence. > > Actually, I have tried to model both the case of only nucleic acids, as > well as the case of protein+nucleic acids. > > (1) Modelling only nucleic acids - results in the following error: > rdpdb___303E> No atoms were read from the specified input PDB file, since > the starting residue number and/or chain id in MODEL_SEGMENT (or the > alignment file header) was not found; requested starting position: FIRST: > @ > > (2) Modelling protein+nucleic acid - results in the following error: > csrrng__299E> Atom index is out of bounds: 7621 7620 > nselat__596E> Atom index is out of range (iatm,natm): 7621 7620 > > I have a question: > Will Modeller allow for modelling only nucleic acids (without protein), or > does it need to have the nucleic acids modelled along with protein? > > I am still unable to model nucleic acids (either by itself or with > protein) using Modeller and would appreciate any suggestions on > corrections/changes to make. > > With thanks and regards > Nisha > > > > > Hello! > > > > Hopefully others will have more detailed responses, but here is > > something that might help you. > > > > In modelling my protein of interest with a ligand I obtained the same > error message as you have. What I had to do was to modifiy the sequence > headers in the alignment file. In the first description line for each > sequence and template, the total number of residues needs to include the > ligand residues. > > > > I am also trying to model a nucleic acid and have succeeded with a > simpler (ATP) ligand just within the last few days. > > > > I will be working on including a tRNA in my model in the next few > days/weeks and will share any useful info and tips. > > > > -Charlotte Habegger-Polomat > > > > > > > > > > nisha(a)ncbs.res.in wrote: > > > >>Hello Modeller Caretaker > >>I request your help with modelling nucleic acids using Modeller. Reading > through the archives, I have done the following: > >>(1) modified the restyp.lib file for Modeller to recognise my 1-letter > codes for the nucleic acids (ADE, THY, GUA, CYT), with the modified > contents of the file as below: > >>112 | ADE | ! | ADE | > >>114 | CYT | + | CYT | > >>120 | GUA | ^ | GUA | > >>136 | THY | & | THY | > >>(2) modified my pdb file to include the 3-letter pdb codes (ADE, CYT, > >> GUA, > >>THY) instead of 1-letter pdb codes (A,C,G,T,) in columns 18-20 of the > residue name, and > >>(3) have used the alignment of the modified nucleic acid codes (as > specified in restyp.lib) in my alignment file. > >>However, I still get a bunch of warnings and a couple of errors; and I > am > >>unable to understand what changes I need to make to model nucleic acids > using Modeller. > >>This is the final error although I cannot find any correction to make to > my alignment file: > >>rdpdb___303E> No atoms were read from the specified input PDB file, > since > >>the starting residue number and/or chain id in MODEL_SEGMENT (or the > alignment file header) was not found; requested starting position: > FIRST: > >>@. > >>I would appreciate your suggestions as to what I am doing incorrectly. > With thanks and regards > >>Nisha > >>_______________________________________________ > >>modeller_usage mailing list > >>modeller_usage(a)salilab.org > >>http://salilab.org/mailman/listinfo/modeller_usage > > > > > > > > > > > ---------- Forwarded message ---------- > From: Leyla Celik <lc(a)chem.au.dk> > To: modeller_usage(a)salilab.org > Date: Wed, 5 Oct 2005 17:39:37 +0200 > Subject: [modeller_usage] DOPE score > Hello, > > Does anyone out there know if it is possible to find a description of the > DOPE > score? I have been searching the manual, the MODELLER web-site and the > www... > > Thanks in advance > Leyla > > > > -- > Leyla Celik > Ph.d. student > Department of Chemistry > University of Aarhus > Langelandsgade 140 > DK-8000 Aarhus C > Denmark > Tel: +45 8942 3869 > e-mail: lc(a)chem.au.dk > > > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Leyla Celik <lc(a)chem.au.dk> > Date: Wed, 05 Oct 2005 10:10:51 -0700 > Subject: Re: [modeller_usage] DOPE score > Leyla Celik wrote: > > Does anyone out there know if it is possible to find a description of > the DOPE > > score? I have been searching the manual, the MODELLER web-site and the > www... > > The description in the manual is at > http://salilab.org/modeller/manual/node155.html > > The method is still in development, so currently that is the only > documentation. A fuller description will be in the DOPE paper when it is > published. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > --

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