Marcelo - there is something very wrong with the data. You dont to
reprocess in other space groups - the P2/mmm symmetry looks convincing but
PHASER says there are 3500 rejections! That is an awful lot - 10 is a more
normal value.
I cant see the image clearly but something is causing problems. Split
crystal? How are you processing it?
The Moments go crazy at high resolution. Maybe try redoing the MR &
refinement all at 3A?
The MR rotation function solution is wonderful, but you need to conside
spacegroups P 21 2 21. and P 21 21 21 .
The translation vector of 0 0.5 0.13 would produce absences along the b
axis.
The screw axes along a and c look safe.
On 11 August 2018 at 19:36, Marcelo Liberato <marcelovliber...@gmail.com>
wrote:
> I am sorry. I forgot to attach the image.
>
> Cheers
>
> Marcelo
>
> Em sáb, 11 de ago de 2018 às 18:31, Marcelo Liberato <
> marcelovliber...@gmail.com> escreveu:
>
>> Dear Eleanor,
>>
>> Thanks for you answer.
>> Indeed, there are clear ice rings in the images (example attached). So, I
>> integrated again (P1, P2 and P222) excluding the resolution ranges 2.28-2.22
>> and 3.70-3.64. I am attaching the log files from aimless, MR and refmac
>> for P2 (in two different cells) and P222 data.
>> I agree that MR seems very good (in all cases), but the final density
>> maps are always bad. Maybe the data has problems that I am not dealing
>> with.
>>
>> Kind regards
>>
>> Marcelo
>>
>> Em sáb, 11 de ago de 2018 às 16:04, Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> escreveu:
>>
>>> This MR looks good to me, but there are serious flaws with the data.
>>> Your secon moment plot from the aimless log has most spectacular spikes
>>> which are always a BAD THING, and the Wilson plot is not very smooth
>>> either..
>>>
>>> As Randy says, try to sort those problems out first.
>>>
>>> Then you have this message:
>>>
>>>
>>> TRANSLATIONAL NCS:
>>>
>>> Translational NCS has been detected at ( 0.000, 0.500, 0.125).
>>> A translation of 0.5 along B will generate pseudo-absences along b so
>>> you can be sure whether there is a scre axis or not..
>>>
>>> The space group is most likely orthorhombic - these indicators are
>>> pretty convincing for P2/mmm - so I dont know why you have chosen P21 as
>>> the spacegroup?
>>>
>>>
>>> Scores for each symmetry element
>>>
>>> Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in
>>> Lattice Cell)
>>>
>>> 1 *0.917 * 8.18 0.82 61009 0.298 identity
>>> 2 * 0.883* 7.85 0.78 100711 0.381 ** 2-fold l ( 0 0 1)
>>> {-h,-k,l}, along original k
>>> 3 *0.921* 8.39 0.84 99542 0.355 *** 2-fold k ( 0 1 0)
>>> {-h,k,-l}, along original l
>>> 4 *0.920* 8.26 0.83 99218 0.320 *** 2-fold h ( 1 0 0)
>>> {h,-k,-l}, along original h
>>>
>>> So my suggestions:
>>> Sort out data problems
>>>
>>> Merge as P2/mmm
>>>
>>> Let MR search select the most likely spacegroup of the 8 possible.
>>>
>>> You cant even limit the b axis to be a screw axis .
>>>
>>> Your refinement behavior looks OK, but the maps will look bad with
>>> spurious reflections in the list..
>>>
>>> Eleanor
>>>
>>>
>>>
>>>
>>>
>>> On 10 August 2018 at 19:02, Eleanor Dodson <eleanor.dod...@york.ac.uk>
>>> wrote:
>>>
>>>> Actually Marcelo - Refinement to an R of 41% is pretty good for an MR
>>>> solution!
>>>>
>>>>
>>>>
>>>> On 10 August 2018 at 18:42, Eleanor Dodson <eleanor.dod...@york.ac.uk>
>>>> wrote:
>>>>
>>>>> Can you attach the refinement log?
>>>>>
>>>>> Eleanor
>>>>>
>>>>> On 10 August 2018 at 16:57, Marcelo Liberato <
>>>>> marcelovliber...@gmail.com> wrote:
>>>>>
>>>>>> Dear Randy,
>>>>>>
>>>>>> Thank you very much for answering. I followed your suggestions but,
>>>>>> unfortunately, I couldn't get a reasonable electron density map after MR
>>>>>> and refinement.
>>>>>>
>>>>>>
>>>>>> First I would look at the data to see if you have ice rings, because
>>>>>>> the peak in mean intensity and second moment of the intensity at about
>>>>>>> 2.25A resolution suggests an ice ring problem. If so, you should make
>>>>>>> sure
>>>>>>> you don't contaminate the data with spurious large intensities.
>>>>>>>
>>>>>>> Indeed, the data has ice rings. At first, I required imosflm to
>>>>>> remove ice rings, but it didn't happened. So, I re-processed the data in
>>>>>> different space groups removing the ice rings.
>>>>>>
>>>>>> Second, the statistics (e.g. the second moments plot after tNCS
>>>>>>> correction in Phaser) would be consistent with a scenario in which you
>>>>>>> have
>>>>>>> pseudosymmetry along with a twin operator that parallels the
>>>>>>> pseudosymmetry. If that's true, it's hard to be sure of the symmetry.
>>>>>>> For
>>>>>>> instance, if the structure really is monoclinic, can you be sure you
>>>>>>> chose
>>>>>>> the correct axis to be the 2-fold?
>>>>>>>
>>>>>>
>>>>>> I am not sure. However, I tried two possible axis to be the 2-fold
>>>>>> and none of them gave me reasonable maps after MR and refinement.
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Since you have a good model that gives clear MR solutions even in
>>>>>>> P21, you can probably process the data in P1 and solve it with 8 copies
>>>>>>> in
>>>>>>> the unit cell. Then you can look at the symmetry of the MR solution
>>>>>>> (e.g.
>>>>>>> in Zanuda) and see whether it obeys any higher symmetry than P1.
>>>>>>>
>>>>>>
>>>>>> I processed data in P1. After MR (with 8 copies in the ASU), it
>>>>>> resulted in TFZ=11.6 and LLG=1434. But the map is still bad and high
>>>>>> Rwork and Rfree.
>>>>>> According to Zanuda, the data should be P21:
>>>>>>
>>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>>>>
>>>>>> | >> 4 | P 1 21 1 | 68.6868 | 0.6289 | 0.5487 | 0.5523 |
>>>>>>
>>>>>> ---------------------------------------------------------------------
>>>>>>
>>>>>> | 1 | P 1 | 69.4151 | 0.6171 | 0.5471 | 0.5559 |
>>>>>>
>>>>>> | 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
>>>>>>
>>>>>> | 11 | P 21 21 21 | 52.0271 | -- | 0.6107 | 0.6178 |
>>>>>>
>>>>>> ---------------------------------------------------------------------
>>>>>>
>>>>>> | << 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
>>>>>>
>>>>>> ---------------------------------------------------------------------
>>>>>>
>>>>>> I processed in P21 using two different unit cells, and MR resulted in
>>>>>> TFZ=20.8 and LLG=511, and TFZ=56 and LLG=2867. However, again, no
>>>>>> good maps and statistics.
>>>>>>
>>>>>> Best regards
>>>>>>
>>>>>> Marcelo Liberato
>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>
>>>
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