hi, i have a few practical questions about density maps and occupancy in structure determination and would appreciate either direct feedback or literature references.
in a structure that i am currently working on via mol rep, i see difference density for a peptide ligand. when i build the ligand and do refinement in REFMAC 5 and look at the 2fo-fc map, I see nice density for the ligand now. but, if I then use the coordinates with the ligand to look at a density modified map within CNS, i only see density for bits of the ligand. does this mean that the 2fo-fc map is wrong or that the peptide ligand is disordered some? Basically, how does one know what maps to trust or not, and why one map might show density where another doesn't. I understand to some degree the model bias in the 2fo-fc map, but this doesn't explain the density observed in the difference map. my other thought was that the ligand could have occupancy less than 1, but I am not sure how this would be treated within density modification in CNS. are there papers explaining how one might determine the occupancy of a ligand and how to work with this situation? any suggestions or references on dealing with density maps or occupancy would be greatly appreciated. thanks in advance for all feedback. cheers, nick ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 [EMAIL PROTECTED] www.noinaj.com
