hi,

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)

In the given example:

>P1;1qg8
structureX:1qg8:   2 :A: 256 :A:undefined:undefined:-1.00:-1.00
PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR
YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW
NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT---------
-----EFVRNLPPQRNCRELRESLKKLGMG*
>P1;1qg8_fill
sequence:::::::::
PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR
YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW
NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF
ELEKNEFVRNLPPQRNCRELRESLKKLGMG*

Here what extra alignment should be added if i have a pdb(b.pdb) with missing residues included which can be used as a template(same sequence).

Also can i add missing residues in both A and B units simultaneously.