Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6

[bharat lal <>]

Thanks for ur help

 

But I am still not able to generate any model as after doing the alignment of the two sequences like teh way u said. Its giving the error "Sequence Difference between the alignement and pdb" . Here is my alignment file :-

 

>P1;template
structureX:template:1    :A: 230 :: :  : :
ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFF-----------NYKTRAEVK
FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED
GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM
DELYK
*

>P1;target
sequence:target:    : :   : : :  : :
ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFTDGYDFNDSKANYKTRAEVK
FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED
GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM
DELYK
*

 

The error is :-

 

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      3567011    3483.409     3.402
read_te_291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position    101)
 Alignment   RTIFFNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG
       PDB   RTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADK
     Match   *****          *                 *    *  *
  Alignment residue type   12 (N, ASN) does not match pdb
  residue type    9 (K, LYS),
  for align code template (atom file template), pdb residue number "101", chain "A"

  Please check your alignment file header to be sure you correctly specified
  the starting and ending residue numbers and chains. The alignment sequence
  must match that from the atom file exactly.

  Another possibility is that some residues in the atom file are missing,
  perhaps because they could not be resolved experimentally. (Note that Modeller
  reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
  In this case, simply replace the section of your alignment corresponding
  to these missing residues with gaps.
read_te_288W> Protein not accepted:        1  template

---------------------------------------------------

 

I am using model-loop.py script to generate the models.

 

i want to know one more thing that how this script will model the structure of the loop sequence since the pdb coordinates are not present in the template file ...

 

 

Regards

---------

 

BHARAT