Hello,
I have been modeling a homopentamer which should have a disulfide bond
in each subunit in the same position as the multiple templates that we
are using (the alignments have the cys residues of the target lined up
with the disulfide-forming cys in the templates). When I carry out the
alignment of the templates using salign, the XX_fit.pdb files for the
templates do not have the disulfides indicated using SSBOND, even though
the original pdb files (XX.pdb) do have the SSBOND lines in them.
I know that automodel will automatically include disulfide restraints
if the templates have them. However,the returned models, while
superimposing nicely on the template structure, do not have the
disulfides, even though the cysteines in the model are right where the
disulfide-forming cysteines are in the template. I assume that automodel
uses the XX_fit.pdb files for the fitting routines, and the fact that
the XX_fit.pdb files are missing the SSBOND lines is why the disulfides
are present in the model.
Is this correct? Can I just edit the XX_fit.pdb files to include the
SSBOND lines to force the model to have the disulfides?
Alternatively, I guess I could use model.patch as per node24 in the
online manual to force the disulfides to be where I want them to be, but
this just doesn't seem right if the templates all have the disulfide and
the alignments have the cysteines where they should be.
Thanks
Mike White
