Dear Modeller team,
I need your quick suggestions and corrections on my scripts that I have been using to run on multiple computers. I am not getting any errors when I run the script3.py. But, when I compare the files .pap and .ali with other alignment servers like muscle, there are aminoacids missing in the alignment with Modeller. I don`t know where is the problem, if it is related to the alignmet with Modeller or if there is a problem in the script.py.
Best regards.
Paul Zair Leyva Miranda Laboratory of Molecular Modeling ESM-IPN
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
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Modeller Caretaker -
Paul Zair Leyva Miranda