Re: [modeller_usage] more sequence difference issues

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