Re: [modeller_usage] Chimeric protein - residue numbers

On 06/05/2012 10:17 AM, Larsson, Per (pl6n) wrote: > I am trying to build a model using the automodel class, based on two > known structures where I want parts of the model to be based on > structure A and parts on structure B.

The sequence for each template in your alignment file must always match the PDB sequence exactly, otherwise Modeller won't know which restraints to extract from the structure. It can't guess that you don't want to use some set of residues just because you missed them out. Either edit the PDB file to remove those residues, or misalign them (i.e. include them in the alignment but align them with gaps in the model sequence, so they're not used).

Ben Webb, Modeller Caretaker