Hi Chen,
if Rmeas is high (like 50 and up) even in P1 then maybe the integration was not
right, or the indexing is offset by 1 in h or k or l ?
To check the former, look at FRAME.cbf and see if the predictions match the
spots.
To test the latter try
echo CENTRE | pointless XDS_ASCII.HKL
best,
Kay
P.S. in XDS's space group determination, Friedels are indeed considered
symmetry-related.
On Wed, 13 May 2015 19:24:30 -0400, Chen Zhao <c.z...@yale.edu> wrote:
>> 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 <merr...@u.washington.edu>
>>>> 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 <merr...@u.washington.edu>
>>>>>> 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
>>>
