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:
Alignment VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQ PDB - - -IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN
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).
Regards!
João [ .. ] Rodrigues
(Blog) http://doeidoei.wordpress.com (MSN) always_asleep_@hotmail.com (Skype) rodrigues.jglm
On Tue, Jul 21, 2009 at 11:47 AM, bharat lal monu46010@yahoo.com 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 :- > Alignment VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQ > PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN > 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 .. > > Bharat > > ------------------------------ > See the Web's breaking stories, chosen by people like you. Check out Yahoo! > Buzz http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/. > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >