ModellerError: read_te_290E> Number of residues in the alignment and pdb files are differen
Hello, i'am struggling for days, i am new with modeller, i'm a grad student in biotechnology area and i'm trying to learn how to use modeller. I'm trying for days to model this sequence but i keep getting this error "modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 3525 4026 For alignment entry: 1 6nzk" follows the alignment.pir file, can anyone tell what can i do to fix that? Thanks
>P1;6nzk structure:6nzk.pdb:15:A:1234:A:::: VIGDLKCTSDNINDKDTGPPPISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGST YRNMALKGSVLLSRLWFKPPFLSDFINGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNT SYSVVVQPRTINKLQGLLEVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKR NFTYDVNADYLYFHFYQEGGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLT LEYWVTPLTSRQYLLAFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQP IADVYRRKPNLPNCNIEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNI DAAKIYGMCFSSITIDKFAIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAAN VSVSRFNPSTWNKRFGFIEDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNNGIGT CPAGTNYLTCTPDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLG WSADSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFV EVNATYYNSWQNLLYDSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRN IKCNYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSTTGYR FTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAFVCGDYA ACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDIN FSPVLGCLGSASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYKGIKVL PPLLSENQFSGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIAN AFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLD ALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGN GNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGYFVNVNNTWMY TGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNVIGDLKCTSDNINDKDTGPPPISTD TVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRLWFKPPFLSDF INGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTIN-------KLQGLL EVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHFYQE GGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLLAFN QDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCNIEA WLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKF AIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFI EDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLN-----------NGIGTCPAGTNY LTCT----PDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSA DSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVN ATYYNSWQNLLYDSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKC NYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYS-------- -TTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAF VCGDYAACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNF NVDDINFSPVLGCLG----SASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLIC VQSYKGIKVLPPLLSENQFSGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDV LSQNQKLIANAFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISA SLQEILSRLDALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKS QSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGY FVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNVIGDLKCTSDNINDK DTGPPPISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRL WFKPPFLSDFINGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTINKLQ GLLEVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHF YQEGGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLL AFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCN IEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITI DKFAIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRF GFIEDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNNGIGTCPAGTNYLTCTPDPI TFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSADSCLQGDKCNIF ANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVNATYYNSWQNLLY DSNGNLYGFRDYITNRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKCNYVFNNSLTRQL QPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSTTGYRFTNFEPFTVNSVNDS LEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAFVCGDYAACKSQLVEYGSFCDN INAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDINFSPVLGCLGSASSRS AIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYKGIKVLPPLLSENQFSGYTLA ATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIANAFNNALYAIQEGFDA TNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAEAQIDRLINGR LTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGL YFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGYFVNVNNTWMYTGSGYYYPEPITENN VVVMSTCAVNYTKAPYVMLN* >P1;cvd sequence:cvd:1:A:1353:A:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------MFLILLISLPTAFA-------------------------------- -----------------------------------VIGDLKCTSDNINDKDTGPPPISTD TVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGSVLLSRLWFKPPFLSDF INGIFAKVKNTKVIKDRVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGDNKLQGLL EVSVCQYNMCEYPQTICHPNLGNHRKELWHLDTGVVSCLYKRNFTYDVNADYLYFHFYQE GGTFYAYFTDTGVVTKFLFNVYLGMALSHYYVMPLTCNSKLTLEYWVTPLTSRQYLLAFN QDGIIFNAEDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPNLPNCNIEA WLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKF AIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFI EDSVFKPRPAGVLTNHDVVYAQHCFKAPKNFCPCKLNGSCVGSGPGKNNGIGTCPAGTNY LTCDNLCTPDPITFTGTYKCPQTKSLVGIGEHCSGLAVKSDYCGGNSCTCRPQAFLGWSA DSCLQGDKCNIFANFILHDVNSGLTCSTDLQKANTDIILGVCVNYDLYGILGQGIFVEVN ATYYNSWQNLLYDSNGNLYGFRDYIINRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKC NYVFNNSLTRQLQPINYFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSKNRRSRGA ITTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMVEFIQTSSPKVTIDCAAF VCGDYAACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNF NVDDINFSPVLGCLGSECSKASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLIC VQSYKGIKVLPPLLSENQISGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDV LSQNQKLIANAFNNALYAIQEGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISA SLQEILSRLDALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKS QSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTARVSPGLCIAGDRGIAPKSGY FVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNTS------------- ------------------------------------------------------------ ---IPNLPDFKEELDQWFKN---------------------------------------- ----------------QTSVAPDLS----------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------LDYINVTFLDLQVEMNRLQEAIKVLNQSYINLKDIGTY--------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------------------EYYVKWP---- ---------------WYVWLLICLAG------------------------------VAML VLLFFICCCTGCGTSCFKKCG------------GCCDDY-------TGYQELVIKTSHDD ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------*
On 4/1/20 10:50 AM, Joao Sartori wrote: > Hello, i'am struggling for days, i am new with modeller, i'm a grad > student in biotechnology area and i'm trying to learn how to use modeller. > I'm trying for days to model this sequence but i keep getting this error > "modeller.ModellerError: read_te_290E> Number of residues in the > alignment and pdb files are different: 3525 4026 For alignment > entry: 1 6nzk"
I'm not sure what you're trying to do here but the alignment file sequence has to match that in the PDB file. You clearly have 3525 residues in the alignment file but you are asking Modeller to read residue 15:A through 1234:A (which does match the A chain range for 6nzk at PDB). Obviously 15-1234 isn't 3525 residues (not sure how you got 4026 unless you edited the PDB file - 6nzk from PDB has 1175 residues).
Ben Webb, Modeller Caretaker
Ok, thanks.
Em qua, 1 de abr de 2020 16:48, Modeller Caretaker < modeller-care@salilab.org> escreveu:
> On 4/1/20 10:50 AM, Joao Sartori wrote: > > Hello, i'am struggling for days, i am new with modeller, i'm a grad > > student in biotechnology area and i'm trying to learn how to use > modeller. > > I'm trying for days to model this sequence but i keep getting this error > > "modeller.ModellerError: read_te_290E> Number of residues in the > > alignment and pdb files are different: 3525 4026 For alignment > > entry: 1 6nzk" > > I'm not sure what you're trying to do here but the alignment file > sequence has to match that in the PDB file. You clearly have 3525 > residues in the alignment file but you are asking Modeller to read > residue 15:A through 1234:A (which does match the A chain range for 6nzk > at PDB). Obviously 15-1234 isn't 3525 residues (not sure how you got > 4026 unless you edited the PDB file - 6nzk from PDB has 1175 residues). > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Joao Sartori -
Modeller Caretaker