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,
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).