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.

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From: CCP4 bulletin board [[log in to unmask]] on behalf of Matthias Barone [[log in to unmask]]
Sent: Friday, October 14, 2016 8:00 AM
To: [log in to unmask]
Subject: [ccp4bb] Antw: Re: [ccp4bb] High B factor

[log in to unmask]" class="GroupWiseMessageBody">

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 all, no?

matthias

 

>>> Pavel Afonine <[log in to unmask]> 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. 

(A joke). 

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         Carlos CONTRERAS MARTEL, Ph.D.
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