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 doesn'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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