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Re:Re: [sdpd] Re: Restraints and so on
>Of course, any crystal structure refinement is partly constrained (at least by the symmetry) but I mean the SDPD cases when constraints or restraints are imposed on ALL structural parameters.
to me, a crystallographic software user.
in my opinion,
Constraints & restraints can not be avoidable in both single crystal diffraction and powder diffraction. So the main point is how and when it can be used properly to get the proper R and chemical, physical and geometry reasonable structure. The answer will be according to structure complex and diffraction data. Just like Professor Armel said the range of d/p.
Thank you for discussion.
Best regards and My apologies,
Xu Jun
At 2011-09-14 19:46:05,"Lubomir Smrcok" <uachsmrk...@savba.sk> wrote:
>I know this is not quite fair to advertise own work, but a nice example
>how can restraints be used to "improve" the results is analysed in
>the survey
>
>"A comparison of powder diffraction studies of kaolin group
>minerals." Zeitschrift fuer Kristallographie (1995) 210, 177-183.
>
>A Commedy of Errors, atlthough not by William S. ...
>
>My apologies,
>lubo
>
>On Wed, 14 Sep 2011, L_Solovyov wrote:
>
>>> It will be hard to define an exact limit
>>> since all determined crystal structures are
>>> more or less wrong,depending on the
>>> degree of accuracy you want to impose, some
>>> parts of the structures being less
>>> accurate than others.
>>
>> Of course, any crystal structure refinement is partly constrained (at least by the symmetry) but I mean the SDPD cases when constraints or restraints are imposed on ALL structural parameters. What validation criteria can be used in such cases ¨C R-factors???...
>>
>> The term "structure optimization" is, indeed, not quite appropriate ¨C a better variant would be "structure speculation".
>>
>>> This suggests also that, as for papers in Acta Cryst where the Fo/Fc are
>>> used for the CheckCIF process, powder works should provide the
>>> raw powder diffraction pattern, giving a chance to the referee to make a
>>> better job - hum again...
>>
>> Not only raw data, but also the parameters file for the refinement program applied, and the refinement program MUST be freely available including the source code. Otherwise - structure speculation, because without source code one can't be sure that the program does not impose some hidden restraints to satisfy a potential user.
>>
>> *******************************************************
>> Leonid A. Solovyov
>> Institute of Chemistry and Chemical Technology
>> 660049, K. Marx 42, Krasnoyarsk, Russia
>> http://sites.google.com/site/solovyovleonid
>> *******************************************************
>>
>> --- In sdpd...@yahoogroups.com, Armel Le Bail <armel.le_bail...@...> wrote:
>>>
>>>
>>>>> we can solve structures much more complex than those we can refine
>>>> without restraints.
>>>>
>>>> If a minimum of a cost function is found for a constrained structure
>>>> model in direct space, but the unconstrained refinement is
>>>> impossible, one does not have criteria (e.g. distances, angles,
>>>> their e.s.u. etc.) to assert that the structure is determined or
>>>> soled. For such cases a special term should be proposed instead of
>>>> structure solution, say, structure optimization.
>>>
>>> Hum, this eliminates almost all proteins, none was determined or
>>> solved, even from
>>> single crystal data, according to your criteria. It will be hard to
>>> define an exact limit
>>> since all determined crystal structures are more or less wrong,
>>> depending on the
>>> degree of accuracy you want to impose, some parts of the structures being less
>>> accurate than others.
>>>
>>> Remember that in the sixties and before, the H atoms were frequently not
>>> located from single crystal data. Even nowadays, people use the structure
>>> solution software (SHELXL, etc) suggestions for obtaining the supposedly
>>> riding hydrogen atoms which coordinates are then "refined" with restraints.
>>> We have no estimation of the percentage of false H atoms which were
>>> "seen". Not speaking of the multitude of structures from single crystal data
>>> that cannot be refined without restraints but are certainly "correct enough".
>>>
>>> So, "structure optimization" should be reserved to more noble works
>>> I think, when there is really an optimization (suggesting a better
>>> final result).
>>> Because if you optimize a wrong model, it will continue probably to be wrong,
>>> which is not the sense I would expect for an optimization. Indeed, quantum
>>> optimization is supposed to say if the model is wrong (hum...).
>>>
>>> Finally, as a conclusion, we can be sure that, with SDPD, we have extended
>>> the domain of the "uncorrect enough" structures... giving them a chance
>>> to be really optimized with sophisticated quantum chemical software, though
>>> probably, false proposals will be in such results as well. Science progressing
>>> (too much ?)...
>>>
>>> This suggests also that, as for papers in Acta Cryst where the Fo/Fc are
>>> used for the CheckCIF process, powder works should provide the
>>> raw powder diffraction pattern, giving a chance to the referee to make a
>>> better job - hum again... Any special PLATON version for powder works ?
>>> I think that very few will pass the tests without a huge list of ALERT A.
>>>
>>> Best,
>>>
>>> Armel
>>>
>>
>>
>>
>>
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