Sir,

Did you mean that i should edit the template(for missing residues) pdb so that it contains the co-ordinates of the missing residues only. ; and the alignment look likes ---------------------mmmmmmmm-------------------* where m stands for missing residues.?

But what you mean by overlap the regions a little so that modeller can figure out the conformation of the missing regions?

Thank you very much for your reply

On Thu, May 3, 2012 at 3:59 PM, Mary Varughese <maryvj1985@gmail.com> wrote:

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.


Thanking you
--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India




--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India