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Re: [modeller_usage] residue problem



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


>>> hemant kushwaha <> 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    &! 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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