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[modeller_usage] ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different



Hello,

I'm trying to model a sequence of alpha beta tubulin based on template (3jar), with ligand included. 

After aligning the template and sequence according to this tutorial:

https://salilab.org/modeller/tutorial/basic.html

I'm doing the model building according to this:

https://salilab.org/modeller/9.20/manual/node18.html

After alignment, I edited my .ali file to look like this (adding the dots corresponding to the hetero atoms): 


>P1;3jar_template
structureX:3jar_template.pdb:   1 :B:+861 :K:::-1.00:-1.00
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDS
VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTL
LISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDL
NHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPR---G--L-K-MSAT-F
IGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQ--YQDAT./MRECISIHVG
QAGVQIGNACWELYCLEHGIQPDGQM-PDS------FNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLF
HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYG
KKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSS
ITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKY
MACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEA
WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE..*

>P1;tetrahymena
sequence:tetrahymena:     : :     : ::: 0.00: 0.00
MREVISIHVGQGGIQVGNACWELFCLEHGI------QPDG--QMDAFNTFFSETGAGKHVPRAVFLDLEPTVIDE
VRTGTYRQLFHPEQLISGKEDAANNFARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVFNSVGGGTGSGLGSL
LLERLSVDYGKKSKLGFTIYPSPQVSTAVVEPYNSILSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNL
NRLIAQVISSLTASLRFDGALNVDITEFQTNLVPYPRIHFMLSSYAPIISAEKAYHEQLSVAEITNSAFEPANMM
AKCDPRHGKYMACSMMYRGDVVPKDVNASIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVMRAVCM
ISNSTAIAEVFSRLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGIETAE./MREIVHIQGG
QCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLF
RPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYP
DRIMETFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSG
VTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCAADPRHGRY
LTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSICDIPPK--------GLKMAVTFVGNSTAIQEM
FKRVAEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ-DAT-..*

I'm getting this error "ModellerError: read_te_290E> Number of residues in the alignment and  pdb files are different:      864      861 For alignment entry:        1  3jar_template".

Thanks a lot.