Re: [modeller_usage] Modeling a structure
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
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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 > >
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bharat lal -
João Rodrigues