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Re: [modeller_usage] more sequence difference issues
- To: Irene Newhouse <irenenew AT hawaii.edu>
- Subject: Re: [modeller_usage] more sequence difference issues
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Thu, 18 Nov 2010 14:21:25 -0800
- Cc: modeller_usage@listsrv.ucsf.edu
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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