Re: Alignment sequence not found in PDB file

[Bozidar Yerkovich <>]

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).
> 
>