Hi Clemens;

I suggest you to extract the sequence using modeller : basically: Read the pdb file  set ADD_SEQUENCE on and write the alignment. And you will see what sequence modeller consider.

As far as I know Modeller never had issues with gap and "/" which correspond to a TER in your pdb file.

 

Eric

 

 

 

>>> "Clemens Steegborn" <cls2001@med.cornell.edu> 3/30/2004 4:55:59 PM >>>

Hi,

I'm using the WINDOWS version of MODELLER6v2

I get the following error when reading the template and alignment files:

>
>TOP_________>   121  107 CHECK_ALIGNMENT
>
>check_a_343_> >> BEGINNING OF COMMAND
>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
doe! sn't understand '/' (using '/' gives an error stating it doesn't know
this residue)!

I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib
file, but that didn't help.

Any suggestions would be appreciated!

Clemens

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