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.)