Hi Natalia, As this is not a phenix-specific question I'll answer here on the CCP4 bulletin board (for questions that are just for phenix it is best to use the phenix mailing list instead).
Your heavy atom sites (and your protein molecule) are repeated millions of times throughout your crystal based on the symmetry of your space group. By convention, all the repeats of a particular site are represented by just one instance. That site could be in any of the symmetry-equivalent positions, but again by convention those sites are usually placed close to the origin, and usually also close to the protein molecule, but sometimes that doesn't happen automatically. So if I understand the problem correctly, you can use the feature in Coot of "Draw/Cell and symmetry/Master Switch: Show Symmetry Atoms" and select Yes. You can then also set the radius within which to show symmetry atoms. This should show the heavy atoms near to the protein molecule. The answer to the specific question you ask about "the origin of coordinates in the file with heavy atoms and the origin of coordinates of the molecular model" is that these origins should be the same. I hope that helps! All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Natalia O [natalie.c...@gmail.com] Sent: Tuesday, April 14, 2015 9:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phenix: heavy atoms 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
