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 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
-----*-----
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 difference 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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