Re: [ccp4bb]: Enforcing a sigma(f) cutoff

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


> The responses to my question, all of which have been very thoughtful and 
> helpful, lead to the following question: what is a statistically 
> significant difference in the R (or R-free) statistic?  If the R and 
> related factors can be influenced by the solvent model, and in fact 
> differ substantially when calculated by different programs, should a 
> difference of 2% in the R or R-free be dismissed as insignificant?  Or 
> is it an indication that the model can still be improved, for instance 
> through careful analysis of omit maps?  I am aware of Ian Tickle's work 
> analyzing the properties of the R-free, but is there other work that 
> discusses these issues?
> 
> Thanks again,
> 
> Mark
> 

  In my experience in any refinement, when you change the program you 
always change the R factors.. ie CNS differs from REfmac5; SFCHECK 
differs from them both, often by 1-2% etc etc..

I dont think R factors are the best measure of a completed structure; 
you dont say what resolutions your trials are at, but different scaling 
options including Bulk solvent corrections can make a huge difference to 
the lower resolution bins. ( Indeed some quoted R factors actually 
exclude these terms, and only give Rfactors from 6-xA say..)
  At the least you need a table of R factor v resolution, wjich you cant 
ge from the PDB.

  I think the reason REFMAC5 reduces the Rfactor is that it does a 
better job with the temperature factors - if you did have this table of 
R v resolution you would see that the outer shells have fallen, not the 
lowest resln ones..

  How much have the coordinates shifted? I suspect very little


  Your work provides a useful leson to us all I think - dont judge 
quality by R factors alone..


  Eleanor