[modeller_usage] Mismatch in the alignment

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

wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww*

>P1;2ABC_fill

sequence:::::::::

GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG

TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP

PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS

GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS

ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH

SKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww

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