Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6 - Sequence difference between alignment and PDB
To: "" <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6 - Sequence difference between alignment and PDB
From: "Schmid, Ralf (Dr.)" <>
Date: Thu, 13 Jan 2011 09:36:24 +0000
Accept-language: en-US, en-GB
Acceptlanguage: en-US, en-GB
Dear Bharat
Please use meaningful headers for your enquiries, this will increase your chances that someone will bother to read them.
As the error message says, the residues in the alignment for your template don't match the residues in the pdb file. You are missing a Lysine, two Asp and a Glycine - pls see below.
>P1;template
structureX:template:1 :A: 230 :: : : :
ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFF-------KDDGNYKTRAEVK
FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED
GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM
DELYK
*
Cheers,
Ralf
============================================
Dr Ralf Schmid
Lecturer in Bioinformatics
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road
Leicester LE1 9HN UK
Tel. +44 (0)116 229 7023
http://www.le.ac.uk/users/rs206/http://www2.le.ac.uk/departments/biochemistry/staff/schmid
============================================
Times Higher Education University of the Year 2008-9
> -----Original Message-----
> From: [mailto:modeller_usage-
> ] On Behalf Of bharat lal
> Sent: 13 January 2011 07:10
> To:
> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6
>
> 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
>