I am mainly a nucleic acid crystallographer and have a very limited experience with proteins and CNS. I am wanting to make a map of a protein-DNA complex that is in the PDB to look at the DNA-protein interface. I have downloaded the structure factors and generated the mtf file. The problem is that ~133 of the 8000 atoms are unobserved/disordered and not in the pdb file. Generate_easy is placing them in the mtf and pdb file based on their bond and angle restraints. How can I avoid this so that I can make a usable maps?
Chad
