On Mon, Aug 19, 2013 at 3:12 PM, Mark Saper <saper@umich.edu> wrote:

What is the preferred method for handling missing residues or residues with zero occupancy, in terms of PBD submission?

I see three options:
Remove them from the model
set occupancy=0 and flag in REMARKs 475 and 480
keep occupancy=1 and allow the temperature factors to climb

I have a disordered region in my molecule which I am restraining to a portion of a structure in which that region is well resolved. There are several residues that have no density in the current refinement, yet I want to keep them in the model. Suggestions?

This came up a year or two ago, and someone (Ed Pozharski?) even did a simple survey. Support was roughly equal for options (1) and (3), with few people backing option (2) (zero occupancy). If the entire residue is missing, as opposed to just the sidechain, I would prefer (1), however.

-Nat