OK, although the issue of non correspondence of SEQRES and ATOM list remains, five models were built. I'll check the quality. On Chimera the structures are, at first sight, as expected.
A question: of the homomer in the pdb I have modeled a subunit only. Should I had best modeled all chains for the homomer? On using Chimera to get the homomer from the homology model, can the BIOMT transformation matrix given in the pdb file (for both crystallographic and non-crystallographic operation) be used with the model?
Thanks francesco pietra
On Thu, Jul 24, 2008 at 11:00 PM, Francesco Pietra chiendarret@gmail.com wrote: > 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 chiendarret@gmail.com 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) >