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).