Thank for that hint - but that wasn't it neither.
However, by shuffling around the lines in my input files, I got things eventually working.
Is it true that the order of the structures in the alignment file has to be the same as that in the SET KNOWNS command (maybe I missed this in the manual)?
Kind regards, Karsten.
On Friday 16 August 2002 19:28, you wrote: > I know this might sound like a wichcraft, but I was just helping a fellow > MODELLER off the list, who had a similar problem, and I found out that > non-visible 'return' sign at the end of his SET OUTPUT_CONTROL line was > causing MODELLER not to read in PDB structure. After I entered 'return' > and deleted the created new empty line (where this coruptet 'return' > simbol was) everything was fine. > > I think this might have to do how some text editors interpret carry-over > ASCII simbol. > > As for more log info, OUTPUT_CONTROL is the only way. Excceptions > are some commands that have switches for their outputs (i.e. LONG, SHORT, > etc). > > Good luck, > Bozidar Yerkovich > > On Fri, 16 Aug 2002, Karsten Suhre wrote: > > Hi! > > > > 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).