Hi, I am trying to model a hetero dimer protein using modeller and I couldnt make it up..
the error which i was not able to rectify is "PROTEIN SPECIFIED IN ALIGN CODES WAS NOT FOUND IN THE ALIGNMENT FILE"
The alignment file is as follows:
>P1;queryAB sequence:queryAB:1: :1691: : : : : MGPRAKTISSLFFLLWVLAEPAENSDFY-----LPGDYLLGGLFSLHANMKGIVHLNFLQ VPMCKEYEVKV-IGYNLMQAMRFAVEEINNDSSLLPGVLLGYEIVDVCYISNNVQPVLYF LAHEDNLLPIQEDYSNYISRVVAVIGPDNSESVMTVANFLSLFLLPQITYSAISDELRDK VRFPALLRTTPSADHHIEAMVQLMLHFRWNWIIVLVSSDTYGRDNGQLLGERVARRDICI AFQETLPTLQPNQNMTSEERQRLVTIVDKLQQ--STARVVVVFSPDLTLYHFFNEVLRQN FTGAV-WIASESWA-IDPVLHNLTELRHLGTFLGITIQSVPIPGFSEF-----------R EWGPQAGPPPL-----SRTSQSYTCNQECDNCLNATLSFNTILRLSGERVVYSVYSAVYA VAHAL----HSLLGCDKSTC-TKRVVYPWQLLEEIWKVNFT-LLDHQIFFDPQGDVALHL EIVQWQWDRSQNPFQSVASYYPLQRQLKNIQDISWHTINNTIPMSMCSKRCQSGQKKKPV GIHVCCFECIDCLPGTFLNHTEDEYECQACPNNEWSYQSETSCFKRQLVFLEWHEAPTIA VALLAALGFLSTLAILVIFWRHFQTPIVRSAGGPMCFLMLTLLLVAYMVVPVYVGPPKVS TCLCRQALFPLCFTICISCIAVRSFQIVCAFKMASRFPRAYSYWVRYQGPYVSMAFITVL KMVIVVIGMLATGLSPTTRTDPDDPKITIVSCNPNYRNSLLFNTSLDLLLSVVGFSFAYM GKELPTNYNEAKFITLSMTFYFTSSVSLCTFMSAYSGVLVTIVDLLVTVLNLLAISLGYF GPKCYMILFYPERNTPAYFNSMIQGYTMRRD-------------------------- / MLGPAVLGLSLWALLHPGTGAPLCLSQQL-----RMKGDYVLGGLFPLGEAEEAGLRSRT RPSSPVCTRFSSNGLLWALAMKMAVEEINNKSDLLPGLRLGYDLFDTCSEPVVAMKPSLM FLAKAGSRDIAAYCNYTQYQPRVLAVIGPHSSELAMVTGKFFSFFLMPQVSYGASMELLS ARETFPSFFRTVPSDRVQLTAAAELLQEFGWNWVAALGSDDEYGRQGLSIFSALAAARGI CIAHEGLV---PLPRADDSRLGKVQDVLHQVNQSSVQVVLLFASVHAAHALFNYSISSRL ---SPKVWVASEAWLTSDLVMGLPGMAQMGTVLGFLQRGAQLHEFPQY-VKTHLALAT-D PAFCSALGEREQGLEEDVVGQRCPQCDCITLQNVSAGLNHHQTFS---VYAAVYSVAQAL HNTLQCNASG----CPAQDPVKPWQLLENMYNLTF-HVGGLPLRFDSSGNVDMEYDLKLW VWQGSVPRLHDVGRFNGSLRTERLKIRWHTSDNQKPVSRCSRQCQEGQVRRVKGFHSCCY DCVDCEAGSYRQNPDDIACTFCGQDEWSPERSTRCFRRRSRFLAWGEPAVLLLLLLLSLA LGLVLAALGLFVHHRDSPLVQASGGPLACFGLVCLGLVCLSVLLFPGQPSPARCLAQQPL SHLPLTGCLSTLFLQAAEIFVESELPLSWADRLSGCLRGPWAWLVVLLAMLVEVALCTWY LVAFPPEVVTDWHMLPTEALVHCRTRSWVSFGLAHATNATLAFLCFLGTFLVRSQPGCYN RARGLTFAMLAYFITWVSFVPLLANVQVVLRPAVQMGALLLCVLGILAAFHLPRCYLLMR QPGLNTPEFFLGGGPGDAQGQNDGNTGNQGKHE--------------------------- ---- * >P1;1ewkAB structureX:1ewkAB:36:A:512:B: : : : ----------------------------RSVARMDGDVIIGALFSVHHQPPAE------K VPERKCGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSS-------- VALEQSIEFIRKP-------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDK TLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCI AHSD---KIYSNAGEKSFDR-----LLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLG VVGEFSLIGSDGWADRDEVIEGYEVEANGG--ITIKLQSPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLENPNFKKVCTG--NESLEENYV----QDSKMGFVINAIYA MAHGLQNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRY DIMNLQY----------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------TEANRYDYVHVGTWHEGVLNIDDYKI / -----------------------------QRSVARMDGDVIIGALFSVHHQPPAE-KVPE RKCGEIREQY---GIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIE FIRKP-----------------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLS DKTLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGL CIAHSDKIYSNAGEKSFDRLLRKLRERL-----PKARVVVCFCEGMTVRGLL--SAMRRL GVVGEFSLIGSDGWADRDEVIEGYEVEANGGITIKLQ-SPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLEN-PNFKKVCTGNESLEENYVQDSKMGFVINAIYAMAHGL QNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDI--- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------MNLQYTEANRYDYVHVGTWHEGVLNID DYKI *
Please help me to overcome this and to get a best model.
thanks in advance.
MUTHIAH. _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop
On 1/2/10 6:56 AM, Muthiah I wrote: > I am trying to model a hetero dimer protein using modeller and I couldnt > make it up.. > > the error which i was not able to rectify is > "PROTEIN SPECIFIED IN ALIGN CODES WAS NOT FOUND IN THE ALIGNMENT FILE"
It is generally impossible to deduce your error without seeing at least your full log file or an archive of your inputs (not cut-and-paste). Fortunately, you sent me the latter (model.zip) in a separate post. When I run the latest version (9v7) of Modeller on that input file, I see the following warning in the log file:
check_for__W> This file (alignment.ali) appears to be in Rich Text Format; Modeller will probably be unable to read it correctly. To correct this, save it in plain text format (also termed "ANSI encoding" on Windows systems).
You will need to save the alignment file (and all other inputs, such as PDB files) in plain text format, as described in the log file. Modeller will not read Rich Text Format, Word documents, or other file formats.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Muthiah I