Re: [modeller_usage] Mismatch in the alignment

7 Jul 2014


      I think I found it. I just had to change '+402' to '+639' to read all of
them.
---Sajeewa
On Sun, Jul 6, 2014 at 10:16 PM, Sajeewa Pemasinghe sajeewasp@gmail.com
wrote:
> Hi everyone,
>
> I am trying to fill 11 missing residues in a protein. 5 of them are at the
> N-terminal and the other 6 are at the C-terminal. Other than that there are
> 9 non-standard residues and 228 waters in the pdb as well.
>
> My alignment file looks as below.
>
>
> >P1;2ABC
> structureX:2ABC:   6 :A:+402 :A:MOL_ID  1;
>
> -----PRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG
> TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP
> PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS
> GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS
> ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH
>
> SKYWRCLQRTTSTAGRSLIEAQTCENE------.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww*
> >P1;2ABC_fill
> sequence:::::::::
>
> GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG
> TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP
> PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS
> GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS
> ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH
>
> SKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
> wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww*
>
> I get the following error when I run the python script.
>
> read_te_290E> Number of residues in the alignment and  pdb files are
> different:      639      402
>               For alignment entry:        1  2ABC
>                                                            x  (mismatch at
> alignment position    403)
> Alignment   QRTTSTAGRSLIEAQTCENE.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
>        PDB    QRTTSTAGRSLIEAQTCENE
>      Match    *********************************
>
> I have been trying many modifications for a few hours now but I just
> cannot figure out what is wrong. I would highly appreciate some advice to
> get around this problem.
>
> Thank you very much
>
> Sajeewa Dewage
>