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
--
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(a)unisa.it
