[ccp4bb]: Re: [o-info] R-sym I/sigI etc...

["Edward A. Berry" <EABerry@LBL.gov>]

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1. Is this a policy of the journal, or the advice of one particular referee?
I didn't see anything in the instructions to authors saying that authors
with Rsym in the last shell above 50% need not submit.

2. The problem is that the journal/referee wants to use the resolution
cutoff as an indicator of the quality of the crystal/structure,
and this interferes with our use of it as a parameter to be chosen 
in optimizing the refinement strategy. It has to be admitted that the 
resolution cutoff is not a useful measure of structure quality if 
90% of the reflections in the last shell are below the noise level. 

Maybe you could publish the structure at say 2.0 A but say in the text 
that in the final refinement an additional 17,000 reflections between 
1.8 and 2.0 A with I/sigma greater than one were used. Or vice versa use all 
the data in the statistics table, but note that the R-sym exceeded 
50% beyond 2.0 A and in the title say "Structure of xyz protein at 2.0 A".

There was a ccp4bb thread ("a simple question of resolution") 
a few months back discussing useful indicators of data resolution, 
and I think the consensus was for the "optical" resolution
as calculated by e.g. CCP4 sfcheck. sfcheck calculates resolution 
and b-factor based on the width of the Patterson origin peak.
This is calculated from the unphased data, making it suitable
for a crystallization paper where you can't give R-free in the 
last shell.
In my experience optical resolution is higher (smaller number)
than even the most liberal d-spacing cuttoff one would use
(after all optical resolution is measuring a different thing)
and so might unfairly impress a referee who is not aware of 
this. Does anyone know a theoretical relation between the 
optical resolution of a dataset and the D-spacing at which 
it is truncated, supposing strong data all the way?

rams@poori.biochem.uiowa.edu wrote:
> 
> Hello All,
> 
> I thought this was a settled issue.  That R-syms and mean I/sigI's are a
> non -ussue and that the best stratety is to include all information.
> 
> I sent a crystallization manuscript with
> R-sym in final shell 60.7 Redundancy 8.1 I/sigI 0.9 9all in the final
> shell).
> 
> Acta D refused to publish it (a crystallization manuscript) unless I cut
> my resolution or my redundancy  to get better R-sym at the outermost shell
> or cut I/sig I at 1.5..
> 
> The catch is as you collect data to this redundancy the data does get
> weaker and I/sigI gets poorer. I personally think this fine as we have
> solved the structure refined etc.. etc.. and everything looks fine.
> 
> So, do I give up to referees request and publish with lower resolution
> cutoff / lower redundancy cutoff etc.. of do I fight or do I just not
> publish the crystallization paper (which is what I am now inclined to
> do)..
> 
> I thought I would poll the web before I decide....
> 
> Thanks.
> 
> Rams.
> 
> --
> S. Ramaswamy
> Department of Biochemistry.
> University of Iowa.
> 
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