Omid Khalouei wrote: > This is the end of my log-file: > > #################################################### > Read the alignment from file : 1ZPA-1A8GA.ali > Total number of alignment positions: 99 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > > 1 1A8GA 99 1 1A8GA Comeon > 2 1ZPA 99 1 1ZPA Comeon > runcmd______> alignment.check() > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL > .\examples\atom_files\1A8GA.pdb > rdpdb___303E> No atoms were read from the specified input PDB file, > since the > starting residue number and/or chain id in MODEL_SEGMENT (or > the alignment file header) was not found; > requested starting position: 1A : > rdabrk__288W> Protein not accepted: 1 > check_a_337E> Structure not read in: 1 > #################################################### > > and here's my alignment file, I followed what I saw on the link that you > sent me. > >> P1;1A8GA > > structureX:1A8GA:1 : :99 : :HIV1 PR: : 1.90: 0.19 > PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD > QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* > >> P1;1ZPA > > sequence:1ZPA:1 : :99 : :HIV1 PR: : 1.90: 0.19 > PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD > QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*
Like I said, your alignment file is incorrect. Furthermore, I can't see how that alignment file could generate that error - are you sure that's the one you're using? The error message says that your alignment file is requesting to read the sequence starting at residue '1A' in a chain with no identifier, while the alignment file you've posted requests to read starting from residue '1' in a chain with no identifier. What I suspect you actually want to do is read from residue '1' in chain 'A'. So your alignment header would look something like structureX:1A8GA:1 :A:99 :A:HIV1 PR: : 1.90: 0.19
Ben Webb, Modeller Caretaker