Even that occupancy refinement seems to be very interesting for
crystallographers, I complete agree with Phoebe.
On 10/14/16 17:38, Phoebe A. Rice wrote:
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.
Let them fly ... at least for protein atoms ...
Carlos
------------------------------------------------------------------------
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Matthias Barone [bar...@fmp-berlin.de]
*Sent:* Friday, October 14, 2016 8:00 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*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 all, no?
matthias
>>> 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.
(A joke).
--
Carlos CONTRERAS MARTEL, Ph.D.
(CR1 CNRS)
carlos.contreras-mar...@ibs.fr
"Bacterial Pathogenesis Group"
Institut de Biologie Structurale
UMR5075 CEA-CNRS-UGA
IBS
Campus EPN
71, avenue des Martyrs
CS 10090
38044 Grenoble CEDEX 9
FRANCE
tel : (+33) (0)4 57 42 86 41
http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
