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Re: [modeller_usage] Including ligand from template

On 4/15/14, 2:05 AM, James Starlight wrote:

I've followed 1st modeller tutorial making alignment of my target
against 1 template (with the inclusion of hetatm from the template). As
the result I've obtained the below alignment

As pointed out already, you haven't told Modeller to put the ligand in 
the model. Is it possible that you modified the 2rh1.pdb file? Your 
template sequence doesn't match the one in 2rh1 from PDB (there's an 
extra sequence in the official PDB from residue 1002:A to 1161:A that 
isn't in yours). Maybe you removed the ligand by mistake too.

	Ben Webb, Modeller Caretaker
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