Hermant; Extract your sequence from the pdb file and your problem will be solved.

Eric

>>> hemant kushwaha ritturajhemant@yahoo.com 4/7/2004 10:00:58 AM >>>

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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