hi all i have a difficulty in modelling a chimeric protein i dont know what is wrong in my ali file or in the top files. plz help. i have enclosed both of my files in it
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# A sample TOP file for fully automated comparative modeling
INCLUDE # include MODELLER routines
SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files
SET ALNFILE = 'alignment.ali' # input file w/ templates and target
SET KNOWNS = '2PIA' '1GVH' '1TVC' '1KRH' '2CND' '1QGA' '1H42' '1FNC' '1RFK' # templates' PDB codes
SET SEQUENCE = 'reduct' # target code
SET STARTING_MODEL = 1
SET ENDING_MODEL = 3
SET HETATM_IO = ON
SET OUTPUT_CONTROL = 1 1 1 1 1
CALL ROUTINE = 'model' # get alignment and a model
>P1;2PIA StructureX:2PIA :8: :320: :Oxido:HUM: : FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW------------- ------------------------------------------------------------- ------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD*
>P1;1GVH StructureX:1GVH :212: A :261:A :oxido:uk2: : ------------------------------------------------------------P D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------*
>P1;1TVC StructureX:1TVC :44:A:248:A :oxidored:uk3: : ---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL----------------------- ------------------------------------------------------------- ----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF FEKF---LPSG-------------------------------------------------- ------------------------------------------------------*
>P1;1KRH StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------*
>P1;2CND StructureX:2CND :145: :257: :oxidored:uk5: : ------------------------------------------------------------- -----------------------------------------------------------GS GITPMYQIIQAVLRDQPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQV KRPEEGWKYSVGFV-TEAVLREHVPEGGDDTLALACGPPPMIQFAISPNLE---------- ------------------------------------------------------------- ------------------------------------------------------*
>P1;1QGA StructureX:1QGA :194:B :231:B :oxidored:uk6: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE Q------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------*
>P1;1H42 StructureX:1H42 :190:A :235:A :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE QKNPQ--GGR--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------*
>P1;1FNC StructureX:1FNC :234: :281: :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------SRE QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI--------------- ------------------------------------------------------------- ------------------------------------------------------*
>P1;1RFK StructureX:1RFK :4: B :91:B :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET*
>P1;reduct Sequence:reduct:1 : :344 : :hypo:unknown: : FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD*