Re: Alignment sequence not found in PDB file

[Bozidar Yerkovich <>]

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).
>