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