17 Oct
2016
17 Oct
'16
10:15 a.m.
Hi Pavel, as I understand, phenix is alrady on route for the 'future improvements' you point out below. That's great news, and an excellent idea to internally have two models for two data sets - that will give phenix much better fine-tuning options for conventional joint refinement or using the X-ray model as reference model. It sounds like a very promising approach. Best, Tim On Saturday, October 15, 2016 11:40:49 AM Pavel Afonine wrote: > >> this is good to hear, and this demonstrates the power of using more data. > >> The only issue here, as I mentioned before, is that in joint XN > >> refinement we refine one single model against two data sets, while > >> ideally it should be two models in order to account for genuine unique > >> information that is contained in X-ray and neutron data. This will be > >> addressed at some point.> > > Out of curiosity, could you elaborate on why it would be preferred to > > refine two separate models? It seems to me, admittedly not having any > > experience with neutron diffraction, that the ultimate goal is to model > > the system of the crystal, and given 2 data sets, we would want to create > > the single model describing the structure in the crystal that best agrees > > with all the available data. Are the neutron and X-ray data so different > > that using them for joint refinement is disadvantageous? > I think I wrote that already in previous email.. Structures > corresponding to two data sets are of course overall similar may be > different in local details: > - Different X-H(D) distances (see figure 4 here: > http://journals.iucr.org/d/issues/2010/11/00/dz5209/index.html) > - Different data collection temperatures: > -- Different B factors; > -- Different visible water structure; > -- Different local disorder (that may be captured as distinct > conformations at low temperature, but may be blurred at higher temperature); > - Different completeness and resolution of one data set may allow > features in one model corresponding to this data set that may not be > supported by the other data set. For example, you may see a well > resolved water with one or two D in neutron map but you may not even see > any water at all in X-ray map, or the other way around. > - etc etc etc. > > So it is advantageous to use both X-ray and neutron data sets together > but these nuances need to be carefully taken care of which isn't the > case in current implementations of joint XN refinement protocols. This > makes a good room for future improvements. > > Pavel > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: [email protected] -- -- 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