Replace the last zero in OUTPUT_CONTROL to 1. That will give you more info...
Bozidar
On Thu, 15 Aug 2002, Karsten Suhre wrote:
> > Hi! > > when I get the following error message, I understand that the sequence in my > PDB file does not correspond to that read from the alignment. Up to know, it > was what had happened, and I always found the problem by trial and error, but > this time .... :-( > > rdpir___648E> Alignment sequence not found in PDB file: 2 ./1EL3.pdb > > Is there some command or switch in modeller to get some more information on > what the problem is? i.e. which amino acid does not match? > > Thank you very much for any hint, > > Karsten. > > > > PS: here my commands: > > SET OUTPUT_CONTROL = 1 1 1 1 0 > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > and the output: > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = > 'all' > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > rdpir___648E> Alignment sequence not found in PDB file: 1 ./1EL3.pdb > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: 8065909 > 7876.864 7.692 > > > PPS: Attached are the input files (there is only one sequence in the alignment > including gaps .. and the PDB file does only contain ATOM lines. That's > because I eliminated all other stuff to see whether the error changes .. it > doesn't, and I compared the sequences between the PDB file and the alignment > - they are identical). > >