[buster-discuss] Exploding R-factors / adjustment of X-ray weight ?

Gerard Bricogne gb10 at globalphasing.com
Tue Feb 14 11:04:12 CET 2017

Dear Thomas,

     Thank you for the feedback confirming that the source of the
problem was a highly incomplete model. We would still be interested in
the reciprocal space correlation plots, to add to our gallery. Would
you mind sending them off-list to buster-develop at globalphasing.com ?

     It is indeed possible to specify a number (and type) of missing
atoms when you are aware of how incomplete your model is, and that is
what we were about to suggest to you if your problem hadn't got solved
in some other way. Good to know that you are now "out of the stew" :-)

     With best wishes,
     Gerard & Clemens.

On Tue, Feb 14, 2017 at 06:23:46AM +0000, Krey.Thomas at mh-hannover.de wrote:
> Dear Clemens and Gerard,
> Thanks a lot for your suggestions – yes, your suspicion about the incomplete model was right – I solved the issues by placing more molecules per AU (currently refining around R of 0.23), which did not drop out of the first MR runs.
> I seem to remember that there was an option (or a macro?), where one could specify the number of missing atoms. Would that have helped in this case? In any case, is there a good rule of thumb, which percentage of the AU one needs to cover to avoid such a behaviour?
> All the best
> Thomas
> Prof. Dr. Thomas Krey
> Hannover Medical School  
> Institute of Virology
> Structural Virology Group
> Carl-Neuberg-Str. 1          
> D-30625 Hannover
> phone: +49 (0) 511 - 532 4308
> email: krey.thomas at mh-hannover.de
> On 2/13/17, 7:56 PM, "Clemens Vonrhein" <vonrhein at globalphasing.com> wrote:
>     Dear Thomas,
>     On Sat, Feb 11, 2017 at 09:29:34AM +0000, Krey.Thomas at mh-hannover.de wrote:
>     > I am refining a 2.6A structure with a relatively large hexagonal
>     > unit cell (~260x260x200). There is no indication for problems in
>     > indexing (e.g., twinning) nor for pseudotranslation and the MR
>     > solution with 5 molecules per AU looks relatively clear (TFZ of
>     > ~31).
>     Is this the number of mol/asu you expect? How homologous/identical and
>     complete is your search model (i.e. is it just main chain? or
>     poly-ALA? or poly-SER?).
>     > Nevertheless, the refinement explodes to R-values of about 0.85,
>     This sounds very much like an incomplete (or very poor) starting
>     model.
>     > but surprisingly the corresponding maps look quite reasonable (so
>     > the molecules do not seem to be placed simply wrong!).
>     Do you see where you need to correct your current model or where you
>     need to build new model? This would be a very good indication of the
>     predictive power of your current phases.
>     Can you send us the reciprocal space CC plot of that refinement,
>     e.g. after
>       graph_autobuster_recipCC -d your-output-dir
>     This might enable us to see what the reason for those high R-values
>     is.
>     > My question is, whether these high R-factors can be temporary and
>     > related to the adjustment of the X-ray weight and should go down at
>     > some point or if there is something more basic that I am doing
>     > wrong?
>     They can be temporary, yes. However they are unlikely to be related to
>     anything to do with the X-ray weight.  We've had multiple cases with
>     poor R-values (and increasing with refinement) while the reciprocal-
>     space CC plots showed values that stayed below a ceiling that was very
>     much less than 1.0, e.g typically 0.5-0.6 instead of the 0.8+ values
>     normally seen with a good model. Their meaning was therefore that the
>     model was systematically incomplete - that is why we want to take a
>     look at your RecSCC plots, to check whether this is the case with your
>     model.
>     Best wishes
>     Clemens & Gerard (for buster-develop)
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