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[sdpd] Re: Restraints and so on
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<p>>It will be hard to define an exact limit<br>
>since all determined crystal structures are<br>
>more or less wrong,depending on the<br>
>degree of accuracy you want to impose, some<br>
>parts of the structures being less<br>
>accurate than others.<br>
<br>
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 ? R-factors???...<br>
<br>
The term "structure optimization" is, indeed, not quite appropriate ? a better variant would be "structure speculation".<br>
<br>
>This suggests also that, as for papers in Acta Cryst where the Fo/Fc are<br>
> used for the CheckCIF process, powder works should provide the<br>
> raw powder diffraction pattern, giving a chance to the referee to make a<br>
> better job - hum again...<br>
<br>
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.<br>
<br>
*******************************************************<br>
Leonid A. Solovyov<br>
Institute of Chemistry and Chemical Technology<br>
660049, K. Marx 42, Krasnoyarsk, Russia<br>
<a href="http://sites.google.com/site/solovyovleonid";>http://sites.google.com/site/solovyovleonid</a><br>
*******************************************************<br>
<br>
--- In <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a>, Armel Le Bail <armel.le_bail...@...> wrote:<br>
><br>
> <br>
> > >we can solve structures much more complex than those we can refine <br>
> > without restraints.<br>
> ><br>
> >If a minimum of a cost function is found for a constrained structure <br>
> >model in direct space, but the unconstrained refinement is <br>
> >impossible, one does not have criteria (e.g. distances, angles, <br>
> >their e.s.u. etc.) to assert that the structure is determined or <br>
> >soled. For such cases a special term should be proposed instead of <br>
> >structure solution, say, structure optimization.<br>
> <br>
> Hum, this eliminates almost all proteins, none was determined or <br>
> solved, even from<br>
> single crystal data, according to your criteria. It will be hard to <br>
> define an exact limit<br>
> since all determined crystal structures are more or less wrong, <br>
> depending on the<br>
> degree of accuracy you want to impose, some parts of the structures being less<br>
> accurate than others.<br>
> <br>
> Remember that in the sixties and before, the H atoms were frequently not<br>
> located from single crystal data. Even nowadays, people use the structure<br>
> solution software (SHELXL, etc) suggestions for obtaining the supposedly<br>
> riding hydrogen atoms which coordinates are then "refined" with restraints.<br>
> We have no estimation of the percentage of false H atoms which were<br>
> "seen". Not speaking of the multitude of structures from single crystal data<br>
> that cannot be refined without restraints but are certainly "correct enough".<br>
> <br>
> So, "structure optimization" should be reserved to more noble works<br>
> I think, when there is really an optimization (suggesting a better <br>
> final result).<br>
> Because if you optimize a wrong model, it will continue probably to be wrong,<br>
> which is not the sense I would expect for an optimization. Indeed, quantum<br>
> optimization is supposed to say if the model is wrong (hum...).<br>
> <br>
> Finally, as a conclusion, we can be sure that, with SDPD, we have extended<br>
> the domain of the "uncorrect enough" structures... giving them a chance<br>
> to be really optimized with sophisticated quantum chemical software, though<br>
> probably, false proposals will be in such results as well. Science progressing<br>
> (too much ?)...<br>
> <br>
> This suggests also that, as for papers in Acta Cryst where the Fo/Fc are<br>
> used for the CheckCIF process, powder works should provide the<br>
> raw powder diffraction pattern, giving a chance to the referee to make a<br>
> better job - hum again... Any special PLATON version for powder works ?<br>
> I think that very few will pass the tests without a huge list of ALERT A.<br>
> <br>
> Best,<br>
> <br>
> Armel<br>
><br>
<br>
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