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
Hello Yuan,
MODELLER should have given you a message about where the alignment is different from the PDB.
Can you paste it here?
Regards,
João [ .. ] Rodrigues
(Blog) http://doeidoei.wordpress.com (MSN) always_asleep_@hotmail.com (Skype) rodrigues.jglm
On Mon, Nov 9, 2009 at 12:17 PM, SHANG Yuan spl@ust.hk wrote:
> 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 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
participants (2)
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João Rodrigues -
SHANG Yuan