Dear All,
I am new to the crystallography and I am seeking for an advice considering data processing. I have a dataset with 2.8 A resolution. I used hybrid substructure search program in phenix, I got the heavy atom sites (selenium), and then I submitted the site to the autosol. With autosol half of the residues were positioned and there are some loops missing, and a part of structure was built as a chain of alanines. Importantly only half of the methionines was built. Now I am trying to build loops manually in Coot. I was able to build one of the loops, and this loop has a methionine residue, so I wanted to check if one of the heavy atom sites agrees with the self-built methionine position. And here I got completely confused, because if I open a pdb file containing my heavy atom sites and at the same time I open the model - the coordinates, they are not placed in one asymmetric unit. I expected that heavy atoms were found, and then basically “on top of them” the model was built. But that’s not what I see. I am missing something basic and important here and I am completely clueless. What is the relation between the origin of coordinates in the file with heavy atoms and the origin of coordinates of the molecular model? Thank you! Natalia
