Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message:
rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb
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The alignment I have is:
>P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM*
>P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV*
>P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV*
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Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb)
Can somebody help me? Thank you very much, Paola
Hi Paola
you must be sure that all the file and code names are correct. So please check if in your top file the pdb file-name is the same as your actual pdb file name, and it is also the same with what you have in your alignment file (pXXXX.pdb ?)
Please delete the dots from your alignmnet file comment line, this might be disturbing
instead of >structureX:pXXXX:.::.::::: use structureX:pXXXX::::::::
Also, in the second entry you have a missing X:
instead of > structure:pAveM:2::211::::: use structureX:pAveM:2::211::::
Also check that if the pdb file contains exactly the same sequence as your alignment file.
in general, you probably have some syntax problem to fix.
best wishes
Andras
> > Dear users, > I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. > When I tell Modeller to execute the "check_alignment" command, I get the following message: > > rdpir___E> alignment sequence not found in PDB file: 1 > ./pXXXX.pdb > > ####################################################################################################################################### > > The alignment I have is: > > >P1;pXXXX > structureX:pXXXX:.::.::::: > CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* > > >P1;pAveM > structure:pAveM:2::211::::: > -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* > > >P1;Ali2 > sequence:Ali2:::::::: > VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* > > ####################################################################################################################################### > > Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) > > Can somebody help me? > Thank you very much, > Paola > > -- > dott. Paola D'Alessio (PhD student) > Universita' degli Studi di Salerno > Dipartimento Scienze Farmaceutiche > via Ponte Don Melillo, 84084 Fisciano (Sa), Italy > tel.+39 089 962822; e-mail: pdalessio@unisa.it
participants (2)
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Andras Fiser -
Paola D'Alessio