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