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;1qg8structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG* > > 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 > >