I begin to understand that there are residues not located in the X-ray
diffraction experiment. If I understand, I should replace such
locations with blanks "-" in the "sequence" PIR only, in the hope that
modeling will fill the gap. I also delete from the whole ali file
(both "structure" and "sequence") all residues before and after those
comprised in the X-ray diffraction experiment.
Still unclear to me is why, even after the above editing, the SEQRES
list does not correspond to the ATOM list. The PDM manual states that
they must correspond, which is the case of tutorial "Basic example.."
provided.
francesco pietra
On Thu, Jul 24, 2008 at 5:54 PM, Francesco Pietra <> wrote:
> I must have posted the same message to a wrong modeller list. Sorry.
>
> I fear to be unable to read published alignments, though both
> alignments and pdb file are from the same publication. What I did is
> to build the ali file by copy/pasting the whole sequence alignment.
> Perhaps a shortcut that is not allowed. The first line copy/pasted for
> "structure" reads:
> ---------------------------------------------MMDLKVDEE---------EVDSGQPVSIQAFASSSTLHGISHIFSYE---------R
>
> the last G being 30.
>
> The corresponding line for "sequence" reads:
>
> ----------------------------------------------MELKAEEE---------EVGGVQPVSIQAFASSSTLHGLAHIFSYE---------R
>
> again, the last G being 30.
>
> These lines (and all following ones in a continuous sequence) were
> copy/pasted to create the two PIR files for ali.
>
> From the pdb corresponding to "structure" the list of residues begins
> with L(42), K(43), A(44), V(45) for chain A, so that I set 42 as the
> starting residue, chain A. I expected a mismatch. In fact the log file
> reads;
>
> read_te_291E> Sequence difference between alignment and pdb :
> x (mismatch at alignment position 1)
> Alignment MMDLKVDEEEVDSGQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLA
> PDB LKRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLN
> Match * * * *
> Alignment residue type 11 (M, MET) does not match pdb
> residue type 10 (L, LEU),
> for align code XXXX (atom file XXXX), pdb residue number "42", 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 XXXX
>
> Thanks for help about this extremely naive doing.
>
> francesco pietra
>
--
Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)