RE: [modeller_usage] problem reading alignment file

["Schweikardt, Thorsten" <>]

Hi Clemens,

the error you describe usually appears when your pdb-
file has some missing aminoacids in respect to the 
sequence you use in the alignment-file. Modeller states
that your pdb contains 392 residues, but your alignment
contains 433. You can use DeepView to open your template
and save its aminoacid-sequence (File-Save-Save Sequence
as FASTA). Compare it to the sequence in your alignment
file, they should be identical. If not, correct the align-
ment. Hope this helps. Concerning the '/' and '-', I have
no problems using them on the linux-version. 

Best wishes,

Thorsten Schweikardt
Molecular Biophysics
University Mainz, Germany



> I'm using the WINDOWS version of MODELLER6v2
> 
> I get the following error when reading the template and 
> alignment files:

>  >openf5__224_> Open       11  OLD  SEQUENTIAL  myt.atm
>  >rdabrk__290E> Number of residues in the alignment and  pdb 
> files are 
> different:      433      392
>  >              For alignment entry:        1
>  >recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
> 
> the problem seems to be that MODELLER doesn't understand the 
> gap residue '-', as it also doesn't understand '/' (using '/' 
> gives an error stating it doesn't know this residue)!
>