Re: [modeller_usage] Alignment missing

On 2/24/14 1:07 PM, Paul Zair Leyva Miranda wrote: > when I compare the files .pap and > .ali with other alignment servers like muscle, there are > aminoacids missing in the alignment with Modeller.

Without actual examples, it's impossible to say for sure, but note that Modeller uses the PDB sequence from the ATOM or HETATM records only (since that's the only structural information available). Other sequence-based methods may use the SEQRES records.

Ben Webb, Modeller Caretaker