Re: Alignment sequence not found in PDB file

[Karsten Suhre <>]

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).