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

["Manfred S. Weiss" <msweiss@embl-hamburg.de>]

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


Dear Mark,

it is indeed a VERY bad idea to enforce ay kind of sigma cutoff.
The maximum likelihood approach does the proper weighting and
anything additional rejections or weighting are not just 
unnecessary, they will make your structure worse (albeit a
possible lower Rfree).

Cheers, Manfred.

P.S. There is a classic paper by Hirshfeld and Rabinovich about
  this. It was published in the early 80s (or 70s) in Acta A.
  I don't recall the exact reference, but I can dig it out for
  you if you are interested.

********************************************************************
*                                                                  *
*                    Dr. Manfred S. Weiss                          *
*                                                                  *
*                         Team Leader                              *
*                                                                  *
* EMBL Hamburg Outstation                    Fon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85                     Fax: +49-40-89902-149 *
* D-22603 Hamburg                   Email: msweiss@embl-hamburg.de *
* GERMANY                       Web: www.embl-hamburg.de/~msweiss/ *
*                                                                  *
********************************************************************


On Fri, 31 Jan 2003, Mark DePristo wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Hello,
> 
> I have a general question about refinement with refmac5.  I've been 
> re-solving a protein structure against its structure factors (obtained 
> from PDB).  One consistent difference between my new structure and the 
> PDB structure is that the PDB structure uses a sigma(f) cutoff of 0.0, 
> as seen in the REMARK in the pdb file:
> 
> REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
> 
> My structure's PDB file, as generated by refmac5, has the line
> 
> REMARK   3   DATA CUTOFF            (SIGMA(F)) : NONE
> 
> For the life in me I cannot figure out how to enforce a sigma(f) cutoff 
> in refmac5.  There are some suggestions (in the archives of ccp4bb) 
> that such a cutoff can introduce artifacts, as the sigma(f) cutoff 
> disproportionately affects the weaker reflections.  Regardless, I am 
> suspicious that this cutoff accounts for the slightly higher R and 
> R-Free values (~ 2%) of my new structure.  Is this a reasonable 
> interpretation?  If so, how can I enforce a sigma(f) data cutoff?
> 
> Thanks,
> 
> Mark
> 
> Mark DePristo
> Ph.D. Candidate
> Dept. of Biochemistry
> Cambridge University
> mdepristo@cryst.bioc.cam.ac.uk
> http://www-cryst.bioc.cam.ac.uk/~mdepristo/
> 
>