Re: [modeller_usage] Alignment

On Mon, Nov 9, 2009 at 12:17 PM, SHANG Yuan <">> 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

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