> Hi Ethan,
>
> Thanks a lot for your detailed information. I am aware that in IDXREF only
> the lattice symmetry was tried to be determined. I went back to check the
> subtrees in IDXREF because even for P1 the Rmeas is very high, meaning that
> the multiple measurements for the same reflections are already very imprecise
> (test resolution 10-5). I therefore am worried about multiple lattices.
>
> Also related to the probability thing you talked about, there is no point
> group has significantly low Rmeas in this case. Or it is just because even P1
> has high Rmeas, so that the highest point group tried were considered to be
> correct? If so, it sounds hard to determine the point group in this case...
>
> Thank you so much,
> Chen
>
>
>>> On May 13, 2015, at 6:48 PM, Ethan A Merritt <[email protected]>
>>> wrote:
>>>
>>> On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote:
>>> Hi Ethan,
>>
>> Sorry, I'm coming in late on this so I might have missed an
>> earlier explanation of exactly what programs are involved.
>>
>>
>>> Yes. My question was simply whether it calculates the statistics
>> ^^^^
>>> from completely unmerged intensities and just compare say h,k,l with
>>> -h,-k,l (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe
>>> so...
>>
>> What is "it"?
>>
>> If you mean the tables in IDXREF.LP, they only report the fit of points
>> to a particular lattice. They do not compare the intensities of
>> potential symmetry mates. Quoting from the program output:
>>
>> Note, that reflection integration is based only on orientation and metric
>> of the lattice. It does not require knowledge of the correct space group!
>> Thus, if no such information is provided by the user in XDS.INP,
>> reflections are integrated assuming a triclinic reduced cell lattice;
>> the space group is assigned automatically or by the user in the last
>> step (CORRECT) when integrated intensities are available.
>>
>> If you mean the output from a later run of pointless/aimless,
>> so far as I know it applies the symmetry operation being tested
>> to all reflections, which means that Friedel/Bijvoet pairs are
>> not compared. But I could be wrong on that point.
>>
>>> And what is a good number? Is 20 % OK? What about 30 % and even higher?
>>
>> Still refering to output from pointless/aimless, the crucial point is not
>> the absolute number but rather how the agreement for the symmetry operation
>> being tested compares to the agreement for the identity operation.
>>
>> For example, here is the output for a lousy data set with a real 2-fold:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Scores for each symmetry element
>>
>> Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice
>> Cell)
>>
>> 1 0.806 6.97 0.70 17852 0.516 identity
>> 2 0.919 7.67 0.77 21302 0.486 *** 2-fold k ( 0 1 0) {-h,k,-l}
>>
>> [snip]
>>
>> Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta
>> ReindexOperator
>>
>> 1 P 1 2/m 1 *** 0.919 7.30 7.30 0.00 0.73 0.00 0.50 0.00 0.1
>> [-h,-l,-k]
>> 2 P -1 0.081 -0.69 6.97 7.67 0.70 0.77 0.52 0.49 0.0
>> [h,-k,-l]
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> In this case the program reports a 0.91 likelihood that the Laue
>> group is P2 even though the Rmeas is horrible.
>>
>> Ethan
>>
>>
>>> Thanks a lot,
>>> Chen
>>>
>>>
>>>>> On May 13, 2015, at 6:07 PM, Ethan A Merritt <[email protected]>
>>>>> wrote:
>>>>>
>>>>> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
>>>>> Hi all,
>>>>>
>>>>> I am sorry about this question which I should have figured out earlier.
>>>>> For
>>>>> point group determination, does the Rmeas consider Fridel pairs
>>>>> differently?
>>>>
>>>> A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
>>>> This pairing is independent of space group.
>>>> So the agreement or lack of agreement between Friedel pairs is
>>>> not informative about selection of point group or space group.
>>>>
>>>> You may be thinking of a Bijvoet pair, which consists of
>>>> [hkl] and the Friedel mate of some symmetry equivalent of [hkl]
>>>> within a particular spacegroup.
>>>>
>>>> But even in the presence of anomalous scattering I think that
>>>> Bijvoet pairs are expected to agree with each other better than
>>>> with a reflection not related by point group symmetry.
>>>>
>>>>> (although I think it should be...) This is because I saw a
>>>>> derivative dataset collected at peak (from a demo) whose Rmeas is quite
>>>>> high (>50 %) for all the space groups tested (including P1). However, the
>>>>> native dataset has only <10 % Rmeas. Should I worry about the derivative
>>>>> dataset? There seems to be multiple lattices in both datasets based on
>>>>> IDXREF.
>>>>>
>>>>> You inputs are really appreciated!
>>>>>
>>>>> Sincerely,
>>>>> Chen
>> --
>> Ethan A Merritt
>> Biomolecular Structure Center, K-428 Health Sciences Bldg
>> MS 357742, University of Washington, Seattle 98195-7742
>>
