I already tried that - even set it to 2. But the fifth flag only controls dynamics memory allocation prints, which is not my problem here. I guess that something in my PDB file doesn't correspond to what modeller expects (my program runs with other PDB files).
Does anybody know which entries modeller reads and checks?
I had a similar problem reading the PIR alignments. You really need to put exactly 9 :'s into the header, and you must give the residues in upper case - while t_coffee writes them out in lower case. That problem I solved by experimentation. What I am seeking here is a way to obtain some more verbose output when modeller has problems reading my input (especially when you modify your alignments by hand errors slip in very easily).
Thanks a lot for giving my problems some consideration,
Kind regards, Karsten.
On Thursday 15 August 2002 23:58, Bozidar Yerkovich wrote: > 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).