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 <div class="gmail_quote">On Thu, May 3, 2012 at 3:59 PM, Mary Varughese <<a href="mailto:maryvj1985@gmail.com" target="_blank">maryvj1985@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> 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: <pre>>P1;1qg8 <a name="137123f195db7bd4_line-2-1"></a>structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00 <a name="137123f195db7bd4_line-3-1"></a>PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR <a name="137123f195db7bd4_line-4-1"></a>YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW <a name="137123f195db7bd4_line-5-1"></a>NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------- <a name="137123f195db7bd4_line-6-1"></a>-----EFVRNLPPQRNCRELRESLKKLGMG* <a name="137123f195db7bd4_line-7"></a>>P1;1qg8_fill <a name="137123f195db7bd4_line-8"></a>sequence::::::::: <a name="137123f195db7bd4_line-9"></a>PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR <a name="137123f195db7bd4_line-10"></a>YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW <a name="137123f195db7bd4_line-11"></a>NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF <a name="137123f195db7bd4_line-12"></a>ELEKNEFVRNLPPQRNCRELRESLKKLGMG*</pre> 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 </blockquote></div> -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India