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.