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 >