Hi,all. I'm new to Modeller. Since I suspect the align result of "align2d()" function, so I just simple recruited a multiple alignment of a domain family, and then I create the "*.ali" file by hand. But when I try to run "automodel" module, and it indicates "E> Sequence difference between alignment and pdb :". I'm sure my sequence in the alignment and pdb are the same since I have succeeded by using the alignment file created by "align2d()" function. I paste my own alignment below:
>P1;myo10fermA structureX:myo10ferm.pdb: 197 :A:+213 :A:::-1.00:-1.00 ---EMTSTVYCHGGGSCKITINSHTTAGEVVEKLIAGLAMADSANMFALFEYNGHVDKAIESR-TVVADVLAKFE KLAATSEVGDLP--WKFYFKLYCFLDTDNVPKDSVEFA-FMFEQAHEAVIHGHHPAP-EENLQVLAALRLQYLQG DYTLH-AAIPPLEEVYSLARLKAR-AAAAEEVS--SARASIIDKWRKF-QGMNQAQAMAKYMALIKEWPGYGSTL F*
>P1;myo7f sequence:myo7f: : : : ::: 0.00: 0.00 SKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISL-KDRFGFSLYIALFDKVSSLGSGSDHVMDAISQCE QYAKEQGAQERNAPWRLFFRKEVFTPW-HNPSEDNVATNLIYQQVVRGVKFGEYRCEKEDDLAELASQQYFVDYG SEMILE------RLLSLVPTYIPDREITPLKN-LEKWAQLAIAAHKKGIYAQRRTDSQ-KVKEDVVNYARFKWPL L*
And the alignment file created by "align2d()":(This works well with automodel)
>P1;myo10fermA structureX:myo10ferm.pdb: 197 :A:+213 :A:::-1.00:-1.00 ---EMTSTVYCHGGGSCKITINSHTTAGEVVEKLIAGLAMADSANMFALFEYNGHVDKAIESRTVVADVLAKFEK LAATSEV--GDLPWKFYFKLYCFLDTDNVPKDSVEFAFMFEQAHEAVIHGHHP-APEENLQVLAALRLQYLQGDY TLHAAIPPLEEVYSLARLKAR/A/AAAEEVSSARASIIDKWRKFQGMNQAQAMAKYMALIKEWPGYGSTLF*
>P1;myo7f sequence:myo7f: : : : ::: 0.00: 0.00 SKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISLKDRFGFSLYIALFDKVSSLGSGSDHVMDAISQCEQ YAKEQGAQERNAPWRLFFRKEVFTPWHNPSEDNVATNLIYQQVVRGVKFGEYRCEKEDDLAELASQQYFVDYGSE MILERLLSLVPTYIPDREITP-L-KNLEKWAQLAIAAHKKGIYAQRRTDSQKVKE--DVVN-YARFKWPLL*
Any advice will be welcome.and Thanks in advance.
Yuan SHANG