Bernie,
but my chi-squares are always near 1.0, so why would I report it? How
close they should be to 1 is open to discussion, of course. The point
is, it is assumed (at least in scalepack) that you adjust your error
model until chi-square~1. I have never seen a statistics table in a
paper which would report chi-suqares.
I am afraid I may be misinterpreting what you were trying to say - I
apologize if that is the case.
Cheers,
Ed.
Santarsiero, Bernard D. wrote:
> You know there is that other funny column with chi^2's. I like to quote
> both. Half of the reviewers will know which column to look at, but you
> will satisfy the other half.
>
> Bernie
>
> On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
>
>> There are two opposing views on this.
>>
>> First: Rmerge doesn't matter. Don't even look into that column in
>> scalepack output, you will be upset over nothing. If you collect twice
>> as much data (360 sweep instead of 180) from the same crystal, your
>> Rmerge will go up due to higher redundancy, but the dataset will
>> actually get better because you measuring every reflection twice more
>> and your I/sigma will increase by ~40%.
>>
>> Second: Rmerge is very important, because if it is, say, 100% (oh,
>> those zeros in the scalepack output) it means that symmetry-related
>> reflections vary by about 100%, so your data is a pile of garbage (at
>> least in that resolution shell). Cut your data at the resolution where
>> Rmerge is 30% and you will be rewarded by really low Rfactors for your
>> final model. Plus, if you keep all the data to where I/sigma~1, your
>> Rmerge is guaranteed to be 0.00 in the output, and what are you going to
>> tell reviewers of your paper?
>>
>> Of course, truth is somewhere in the middle. If I collect on two
>> crystals of the same type (assuming everything else is the same, such as
>> redundancy), and one has much higher Rmerge, then I should probably
>> choose the other one. If you cut resolution at I/sigma~1, and your
>> overall Rmerge is about 10%, I think it's normal. But if it's 30%, you
>> may have some unusually high level of noise in your data (satellite
>> crystal? twinning? evil xray fairy messing with you?). So Rmerge does
>> tell you something, but only in context with all the other information.
>> After all, the only thing that matters is if your electron density map
>> is interpretable. I dare to say that the quality of the map you get
>> does correlate with Rmerge, but would I discard a dataset just because
>> Rmerge is high without trying to solve the structure and take a look at
>> the density? Never.
>>
>> Cheers,
>>
>> Ed.
>>
>> 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
>>>
>> --
>> Edwin Pozharski, PhD, Assistant Professor
>> University of Maryland, Baltimore
>> ----------------------------------------------
>> When the Way is forgotten duty and justice appear;
>> Then knowledge and wisdom are born along with hypocrisy.
>> When harmonious relationships dissolve then respect and devotion arise;
>> When a nation falls to chaos then loyalty and patriotism are born.
>> ------------------------------ / Lao Tse /
>>
>>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
