Re: [modeller_usage] more sequence difference issues

[Modeller Caretaker <>]

On 11/18/10 12:54 PM, Irene Newhouse wrote:
> In the interests of appearing to make progress, I dropped the alignment
> of which I wrote an hour or so ago from the mulitple alignments
> considered. Now I have another sequence difference issue with 1x06.pdb.

Robert's answer is spot on. Modeller only deals with structural 
information from templates, so it reads the PDB sequence from the 
ATOM/HETATM records, not SEQRES, and that's the sequence that needs to 
match your alignment file.

You may also find FAQ #17 useful here:
http://salilab.org/modeller/FAQ.html#17
It also includes a Modeller script to extract the sequence from a PDB file.

	Ben Webb, Modeller Caretaker
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