[phenixbb] XN-refinement

Tim Gruene tim.gruene at psi.ch
Mon Oct 17 05:15:23 PDT 2016

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.


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
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297


-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 173 bytes
Desc: This is a digitally signed message part.
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20161017/35a89575/attachment.sig>

More information about the phenixbb mailing list