Interesting way to look at it. But those loop residues are really in the
crystal with an occupancy of 1, so wouldn't letting the B factor fly give a
clearer description of what's in the crystal? Especially as many people know
to color the structure by B factors to get a feel for which bits are wiggly,
but they'll never think to color it by occupancy.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias Barone
Sent: Friday, October 14, 2016 8:00 AM
Subject: [ccp4bb] Antw: Re: [ccp4bb] High B factor
Picking up the mail of Pavel, Phenix refines occupancies..
If you expect the loops to be disordered, did you try to lower the occupancy of
these residues, following Ethan Merritt statement that "general uncertainty
[...] is represented better by occupancy <1 rather than an arbitrary large B
factor" (To B or not to B, doi:10.1107/S0907444911028320).
If this attempt does not bring the B-factors down, it will surely make the
model more accurate, as the atom coordinates of the loops may not be correct at
>>> Pavel Afonine <pafon...@gmail.com> 14.10.16 9.36 Uhr >>>
If you are still worry about your Bfactor, you could try TLS,
Or NCS, but SA with MLHL might be better.