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.
Best, Tim 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 ... > > 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 -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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