Hi
I am trying to use modeller to rebuild 5 missing resdiues from a protein that I wish to do some MD on. Whilst I have managed to do this, the x, y and z corrdinates of the modeller output models are all slightly different for each atom for the region of the protein of known structure (i am modelling the sequence against its structure minus the 5 residues). As I was hoping to add to this new complete structure the coordinates of the ligands in the original pdb file, I was wondering if there is any way to define that all the coordinates should be excactly the same as those from the original structure and the only alterations would be the addition of the positions of the 5 'new' residues.
Thanks
Jo