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Re: [modeller_usage] Modeling a structure

Dear Bharat Lal,

As you see the model sequence is shifted a little bit towards the PDB sequence. Try to add three gaps in the beginning of the PDB alignment like this:


Still I think you're going to have problems with some insertions. The PDB doesn't quite match the alignment you have there (insertion: SHTQSVSSKQKVTG).


João [ .. ] Rodrigues

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On Tue, Jul 21, 2009 at 11:47 AM, bharat lal <" target="_blank">> wrote:
I am modeling the structure of of leptin protein using template as 1AX8 protein with PDB file starting with the 3rd residue .. and I am getting the following error :-

     Match                 *                                     ***
  Alignment residue type   18 (V, VAL) does not match pdb
  residue type    8 (I, ILE),
  for align code 1AX8 (atom file 1AX8), pdb residue number "3", 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  1AX8

Cn u pls help regarding this ..


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