In my feeling, lowering the occ explains much more such unordered loops (or
solvent exposed sidechains..).
B-factors are a measure of uncertainty of the atom position xyz: Letting
B-factors fly is like broadening a distribution to an extent where the
expectation value looses its purpose. That in mind, I have no problem reducing
the occ of a solvent-exposed lysine to 30% or even 10% if the atoms are not
even visible in a FEM map...
>>> Tim Gruene <tim.gru...@psi.ch> 17.10.16 10.06 Uhr >>>
Dear Carlos and Phoebe,
the B-value describes the movement of an atom at first order approximation,
i.e. as a harmonic motion. It's very unlikely that an atom that is not visible
in density, discribes a harmonic motion.
It never occurred to me, but modelling disorder by strong B-factor restraints
and refining the occupancy seems quite a good idea and would be a much better
model than an explosion of B-factors.
Coot marks atoms with reduced occupancy, hence there is no extra work required
to visualise reduced occupancy. I am aware that some people use graphics
rendering machinery to work with PDB files instead of a dedicated program like
Coot, but you can never suit everyone.
On Monday, October 17, 2016 09:35:02 AM Carlos CONTRERAS-MARTEL wrote:
> 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 ...
> > ------------------------------------------------------------------------
> > *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)
> "Bacterial Pathogenesis Group"
> Institut de Biologie Structurale
> UMR5075 CEA-CNRS-UGA
> Campus EPN
> 71, avenue des Martyrs
> CS 10090
> 38044 Grenoble CEDEX 9
> tel : (+33) (0)4 57 42 86 41
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Biology and Chemistry
CH-5232 Villigen PSI
Phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A