On 5/3/12 3:29 AM, Mary Varughese wrote: > I have a dimer protein with missing residues in both subunits. > > I have the target sequence, the original protein pdb with missing gaps > *(a.pdb* resolution 3.58 Xray structure)and another pdb of the same > protein with missing residues included (*b.pdb* resolution 3.5 electron > diffraction) > > So i have to add missing residues with b.pdb as the template and rest of > the protein exact to a.pdb)
Yes, that should be fairly straightforward - simply use both templates in modeling, and align the model with a.pdb or b.pdb accordingly. If possible, try to overlap the regions a little so that Modeller can figure out the conformation of the missing regions.
> Also can i add missing residues in both A and B units simultaneously.
Sure, that's no problem. Your alignment might look something like:
>P1;a ... AAAAAAAAAA------AAAAAAAAAA/AAAAAAAAAA------AAAAAAAAAA* >P1;b ... --------BBBBBBBBBB--------/--------BBBBBBBBBB--------* >P1;model ... MMMMMMMMMMMMMMMMMMMMMMMMMM/MMMMMMMMMMMMMMMMMMMMMMMMMM*
(This assumes that you've edited b.pdb to only include the regions in the alignment above.)
Ben Webb, Modeller Caretaker