Truncate reports I/sigI for reflections in the 30deg cones around the
reciprocal cell axes. Dead handy...
[log in to unmask] wrote:
> High R "merges" with no reasonable excuse can certainly be a useful
> red flag during data processing (along with the % of observations
> rejected, which I've never had a reviewer request).
>
> Which brings up the point that one reasonable excuse is anisotropy -
> high Rs for merging random observations in the "imaginary" direction
> will be combined with lower Rs for merging decent data in the "real"
> direction.
> Is there any extant software that will calculate directionally-binned
> Rmerges? It would be useful both for re-assuring users that there
> isn't anything worse with their data, and for arguing with referees
> who don't read CCP4BB.
>
> Phoebe
>
> At 01:18 PM 1/18/2008, Mischa Machius wrote:
>> OK, that brings us back to a more substantial question: is any of
>> these R values actually suitable to judge the quality of a given
>> dataset? Instead of introducing novel R factors, one could also simply
>> ignore them altogether, make sure that the error models have been
>> properly chosen and look at I/sigma(I) as the main criterion.
>> [QUOTE ]If anyone then still wants to present low R factors, one can
>> always divide by 2, if necessary. [/QUOTE]
>>
>> Best - MM
>>
>>
>> On Jan 18, 2008, at 1:02 PM, Salameh, Mohd A., Ph.D. wrote:
>>
>>> Thank you all, it was very, very helpful discussion. However, I
>>> collected crystal data and the Rmerge overall was very high around
>>> 0.17
>>> at 2.6A resolution and I'm wondering what is the acceptable value
>>> (range) of R-merge that worth the time to continue processing! Very
>>> anxious to hear your thoughts. Thanks, M
>>> ****************************************************
>>> Mohammed A. Salameh, Ph.D.
>>> Mayo Clinic Cancer Center
>>> Griffin Cancer Research Building
>>> 4500 San Pablo Road
>>> Jacksonville, FL 32224
>>> Tel:(904) 953-0046
>>> Fax:(904) 953-0277
>>> [log in to unmask]
>>> ****************************************************
>>>
>>>
>>> -----Original Message-----
>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>> Chris Putnam
>>> Sent: Friday, January 18, 2008 1:21 PM
>>> To: [log in to unmask]
>>> Subject: Re: [ccp4bb] differences between Rsym and Rmerge
>>>
>>> On Friday 18 January 2008 09:30:06 am Ethan A Merritt wrote:
>>>>
>>>> Rmerge is an average over replicate measurements of the intensity for
>>>> identical [hkl]. Rsym is an average over the measurements for all
>>> symmetry
>>>> equivalent reflections.
>>>>
>>>> In the presence of anomalous scattering, Rsym will be higher than
>>> Rmerge
>>>> because the Bijvoet pairs, although symmetry related, do not have
>>> identical
>>>> intensities.
>>>>
>>>> One might logically report two values for Rsym, one which averages
>>>> over the Bijvoet-paired reflections and one which does not.
>>>
>>> This has been an eye-opening discussion for me. I've been really
>>> surprised
>>> that there's been such a diversity of opinion about what these common
>>> terms ought to refer to, and the fact that my understanding was wrong.
>>> I always thought that Rsym was an average over all symmetry equivalent
>>> reflections from the same crystal (including Bijvoet pairs) and Rmerge
>>> was
>>> properly restricted to cases of multi-crystal averaging. (My versions
>>> of
>>> Table 1's from single crystals have used "Rsym" rather than "Rmerge".)
>>>
>>> I wonder if the problem here is that the terms have become overloaded
>>> (and
>>> hence non-specific). In that sense "Rmerge" is a particularly
>>> unfortunate
>>> name as every R that we're discussing is a really a merge of some sort
>>> or
>>> another. (In the most naive sense, "Rmerge" might be thought to be
>>> the
>>> R
>>> for whatever variation of reflection merging the experimenter
>>> chooses to
>>> do.)
>>>
>>> One possible solution would be to push the community towards a new set
>>> of
>>> terms with clearly defined meanings (and whose names would be used
>>> explicitly by new releases of MOSFLM, HKL2000, etc. and changes for
>>> new entries in the PDB).
>>>
>>> If new terms were to be adopted, they ought to specifically
>>> distinguish
>>> between single crystal and multi-crystal merging. I see three such
>>> R values that might be useful (I've arbitrarily chosen names to
>>> distinguish
>>> them from each other and the older terms):
>>>
>>> Rhkl - R of identical hkl's
>>>
>>> Rrot - R of symmetry-related hkls, but not Bijvoet pairs
>>> ("rot" coming from the concept that all symmetry-related
>>> reflections can be found via rotations in reciprocal space and
>>> the fact that "sym" has already been used)
>>>
>>> RBijvoet - R of symmetry-related and Bijvoet-related hkls
>>> (including reflections related by both rotations and an inversion
>>> center in reciprocal space)
>>>
>>> Rhkl,multi - multi-crystal version of Rhkl
>>>
>>> Rrot,multi - muti-crystal version of Rrot
>>>
>>> RBijvoet,multi - multi-crystal version of RBijvoet
>>>
>>> The downside of adopting new names is that it makes the previous
>>> literature
>>> obsolete, but I wonder if the older terms were ambiguous enough that
>>> that's
>>> not such a problem.
>>>
>>>
>>> --
>>> Christopher Putnam, Ph.D.
>>> Assistant Investigator
>>> Ludwig Institute For Cancer Research
>>
>>
>> --------------------------------------------------------------------------------
>>
>> Mischa Machius, PhD
>> Associate Professor
>> UT Southwestern Medical Center at Dallas
>> 5323 Harry Hines Blvd.; ND10.214A
>> Dallas, TX 75390-8816; U.S.A.
>> Tel: +1 214 645 6381
>> Fax: +1 214 645 6353
>
> ---------------------------------------------------------------------------------------------------------------------------
>
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> fax 773 702 0439
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>
> http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
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