I usually leave them in although their position is so uncertain; they probably have multiple conformations but that is hard to model at 2.8A . But that is not a hard and fast rule - lots of people set the occupancy to 0.00 and check whether the later maps give better guideance.. Eleanor
On 21 February 2013 10:53, Urmi Dhagat <[email protected]> wrote: > I have a question about B-factors and occupancies of side chains - I am > working on a 2.8 A structure which is missing density for some of the side > chains (especially the floppy ones like Lysine/Argenine, Glutamine) in loop > regions and the B-factors for these side chains are over 100. > I was wondering if it is ok to drop the occupancies of these residues or > side chains to lower their B-factors? Or do I leave them as is? > > Urmi Dhagat >
