Hi all,

I am trying to model my protein on two templates except in a small region in the middle of my sequence which I want to model on a third template only. I have altered the .ali files so that there are gaps in the correct parts of the alignments and changed the pdb files to have corresponding gaps. When I run this it comes up with an error and doesn't make a _fit file:

fit2xyz_296E> Number of equivalent positions < 3: 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

If I don't model this small piece and leave the gaps in the other templates it works fine so this suggests that there is something wrong with the third template or how I assigned it but I cannot figure it out.

Any help would be greatly appreciated as I have a deadline approaching! Thanks!

Below are the .ali and .top files

>P1;1XFD structureX:1XFD:127:A:849:A:::: ------------------------------------------------------------ ---------------------QKKKVTVEDLFSEDFKIHDPEAKWISDTEFIYREQKGTV RLWNVETNTSTVLIEGKKIESLRAIR--YEISPDREYALFSYNVEPIYQHSYTGYYVLSK IPHGDPQSLDPPEVSNAKLQYAGWGPKG-QQLIFIFENNIYYCAHVGKQAIRVVSTG--- ---KEGVIYNGLSDWLYEEEILKTHIAHWWS------PDG-------------------- -----------------------PSISLHVIGLN--------GPTHDLEMMPPDDPRMRE YYITMVKWATSTKVAV-TWLNRAQNVSILTLCDATTGVCTKKHEDESEAWLHRQN----- -------------------EEPVFSKDGRKFFFIRAIPQGGRGKFYHITVS--------- -----SSQPNSSNDNIQSITSGDWDVTK----ILAYDEKGNKIYFLSTEDLPRRRQLYSA NTVGNFNRQCLSCDLVEN-CTYFSASFSHSMDFFLLKCEGPGVPMVTVHNTTDKKKMFDL ETNEHVKKAINDR--QMPKVEYRDIEIDDYNLPMQILKPATFTDTTHYPLLLVVDGTPGS QSVAEKFE--VSWETVMVSSHGAVVVKCDGRGSGFQGTKLLHEVRRRLGLLEEKDQMEAV RTML-KEQYIDRTRVAVFGKDYGGYLSTYILPAKGENQGQTFTCGSALSPITDFKLYASA FSERYLGLHGLDN--RAYEMTKVAHRVSALEEQQFLIIHPTADEKIHFQHTAELITQLIR GKANYSLQIYPDESHYFTSSSLKQHLYRSIINFFVECFRI----------------*

>P1;1H2W structureX:1H2W:208:A:250:A:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------QKLYYHVLGTDQSEDILCAE FPDEPKWMGGAELSDDGRYVLLS------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------*

>P1;1N1M structureX:1N1M:39:A:764:A:::: ------------------------------------------------------------ ---------------------SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENN-I LVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYD LN---KRQLITEERIPNNTQWVTWSPVG-HKLAYVWNNDIYVKIEPNLPSYRITWTG--- ---KEDIIYNGITDWVYEEEVFSAYSALWWS------PNG-------------------- -----------------------PTVKFFVVNTDSLSS---VTNATSIQITAPASMLIGD HYLCDVTWATQERISL-QWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVG- ---------------RFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQID---------- ------------KKDCTFITKGTWEVIG----IEALTSDYLYYISNEYKGMPGGRNLYKI QLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVL EDNSALDKMLQNV--QMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCS QKADTVFR--LNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAA RQFS-KMGFVDNKRIAIWGWSYGGYVTSMVLG----SGSGVFKCGIAVAPVSRWEYYDSV YTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVD VGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFS-----------------*

>P1;DP8mod sequence:DP8mod:.:.:.:.:::: MAAAMETEQLGVEIFETADCEENIESQDRPKLEPFYVERYSWSQLKKLLADTRKYHGYMM AKAPHDFMFVKRNDPDGPHSDRIYYLAMSGENRENTLFYSEIPKTINRAAVLMLSWKPLL DLFQATLDYGMYSREEELLRERKRIGTVGIASYDYHQGSGTFLFQAGSGIYHVKDGGPQG FTQQPLRPNLVETSCPNIRMDPKLCPADPDWIAFIHSNDIWISNIVTREERRLTYVHNEL ANMEEDARSAGVATFVLQEEFDR-YSGYWWCPKAETTPSGGKILRILYEENDESEVEIIH VTSPMLETRRADSFRYPKTGTANPKVTFKMSEIMIDAEGRIIDVIDKELIQPFEILFEGV EYIARAGWTPEGKYAWSILLDRSQTRLQIVLISPELFIPVEDDVMERQRLIESVPDSVTP LIIYEETTDIWINIHDIFHVFPQSHEEEIEFIFASECKTGFRHLYKITSILKESKYKRSS GGLPAPSDFKCPIKEEIAITSGEWEVLGRHGSNIQVDEVRRLVYFEGTKDSPLEHHLYVV SYVNPGEVTRLTDRGYSHSCCISQHCDFFISKYSNQKNP-HCVSLYKLSSPEDDPTCKTK EFWATILDSAGPLPDYTPPEIFSFESTTGFTLYGMLYKPHDLQPGKKYPTVLFIYGGPQV QLVNNRFKGVKYFRLNTLASLGYVVVVIDNRGSCHRGLKFEGAFKYKMGQIEIDDQVEGL QYLASRYDFIDLDRVGIHGWSYGGYLSLMALMQ----RSDIFRVAIAGAPVTLWIFYDTG YTERYMGHPDQNEQGYYLGSVAMQAEKFPSEPNRLLLLHGFLDENVHFAHTSILLSFLVR AGKPYDLQIYPQERHSIRVPESGEHYELHLLHYLQENLGSRIAALKVI--------*

INCLUDE # Include the predefined TOP routines

SET ALNFILE = 'C:\Program Files\Modeller7v7\Models\DP8mod.ali' # Alignment filename SET KNOWNS = '1XFD' '1H2W' '1N1M' # Code of the template SET SEQUENCE = 'DP8mod' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1

SET DEVIATION = 4.0 # Amount of randomization between models

SET LIBRARY_SCHEDULE = 1 # thorough VTF schedule SET MAX_VAR_ITERATIONS = 300

SET FINAL_MALIGN3D = 1 # MALIGN3D and write superposed # templates & models SET MD_LEVEL = 'refine_1' # thorough MD annealing

CALL ROUTINE = 'model'