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