respected sir,

I am having a problem that my alignment file has some
residues missing than in the pdb file. Therefore
modeller is giving the following error:

Read the alignment from file       : alignmenttest.ali
Total number of alignment positions:   970

# Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
1       1BDG     440      1        1BDG undefined
2       1DGK     898      1        1DGK undefined
3       1CZA     898    &! nbsp; 1        1CZA undefined
4       1BG3     887      1        1BG3 undefined
5       1HKC     896      1        1HKC undefined
6       1IG8     458      1        1IG8 undefined
7       1Str     493      1        1Str Candida
albicans
TOP_________>   121 107 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11 OLD SEQUENTIAL
./1BDG.pdb
rdabrk_! _291E> Sequence difference between alignment
and pdb :

   STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES
-----*-----
           1       1        10     LEU       14   GLN
-----LFEKVV
rdabrk__288W> Protein not accepted:        1
openf5__224_> Open       11 OLD SEQUENTIAL
./1DGK.pdb
openf5__224_> Open       11 OLD SEQUENTIAL
./1CZA.pdb
openf5__224_> Open       11 OLD SEQUENTIAL
./1BG3.pdb
rdabrk__291E> Sequence difference between alignment
and pdb :

   STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES
-----*-----
       &nbs! p;   4       1         3     ASP       11   MET
-----DDQVKK
rdabrk__288W> Protein not accepted:        4
openf5__224_> Open       11 OLD SEQUENTIAL
./1HKC.pdb
rdabrk__291E> Sequence difference between alignment
and pdb :

   STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES
-----*-----
           5       1        18     VAL        3   ASP
-----VKKIDK
rdabrk__288W> Protein not accepted:        5
openf5__224_> Open       11 ! OLD SEQUENTIAL
./1IG8.pdb
rdabrk__291E> Sequence diff erence between alignment
and pdb :

   STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES
-----*-----
           6       1         9     LYS       12   ASN
-----KELMQQ
rdabrk__288W> Protein not accepted:        6
check_a_337E> Structure not read in:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1
     1

How can this problem be solved, that modeller should
read pdb file with respect to residue position in
alignment

regards
hemant

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