Modellers,
I would like base a
homology model for a tetrameric transmembrane protein based on a second
homology model of a related protein.
The template model
consists of 4 chains, each with 6 helices.
Loops between several of the helices have been omitted.
I have used my own
alignment and restricted the helical regions using the spatial restraints.
Because the template
contains all 4 chains, I have modelled them together
instead of just one.
However, the model
that results is not symmetric across the subunits/chains.
What is the preferred
way to preserve symmetry in a case like this?
Also, because the
loops are omitted in the template, I have used chain breaks “/” in
the target and gaps “-“ in the template to reproduce the
breaks. That works but then the chain
information is lost in the target.
How can I preserve the
chain information? And can I renumber
segments of the target during the modelling
procedure?
Thanks,
David