On 12:29 Thu 24 Mar , Dale Tronrud wrote:
Of the possible ways to represent this common situation I think placing a side chain with occupancy set to zero is the worst. For the naive user (and that is not necessarly pejorative) it will lead them to view the placement of those atoms as unwarrantably confident. For those with a deep understanding of the meaning of the parameters it is flat wrong - it says that I know that this atom is never in this location.
If you want to be precise for the knowledgeable user you need to put in a non-zero occupancy but assign it a very large sigma on your SIGATM record for that atom. Of course when naive users see SIGATM records I expect their heads will explode.
Has anyone thought about putting them into a second MODEL record instead? That way, they're present for people who want them, but aren't shown by default in programs like PyMol. No clue how refinement programs would deal with this. -- Thanks, Donnie Donald S. Berkholz, Ph.D. Research Fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 office: 507-538-6924 cell: 612-991-1321