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RE: [sdpd] Re: Are restraints as good as observations ?
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<p>Hi all,<br>
<br>
I have been following the tennis match going on here, and I'll point out what Brian Toby said again - use the data you have to fit what you can. When my work strongly focused on this I too used to be stuck on the fact that macromolecular crystallographers can use ultra-low resolution data... until I figured out they're not doing the same thing as people doing large small molecule work. <br>
<br>
So on the reliability of structures, how reliable is a DFT optimized structure... I know that theoreticians can calculate and optimize almost anything, which does not mean the result has any bearing on reality. Is it a result that was DFTized more reliable than a poorly converging result based on experimental data from a fit? And if you want to discuss the philosophy of restraints/constraints, we were not the ones that invented Tikhonov regularization and Levenberg-Marquardt fitting - sometimes when fitting a Jacobian with a poor quality number it is the only way to approach a stable solution...<br>
<br>
Alex Y<br>
_______________________________<br>
Dr. Alexandre (Alex) F. T. Yokochi<br>
Associate Professor of Chemical Engineering<br>
Laboratory for innovative Reaction Engineering for Materials and Sustainability (iREMS lab)<br>
School of Chemical, Biological and Environmental Engineering<br>
Oregon State University<br>
Corvallis, OR 97331 - 2702<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a> [mailto:<a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a>] On Behalf Of Leonid Solovyov<br>
Sent: Thursday, August 01, 2013 4:33 PM<br>
To: <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a><br>
Cc: <a href="mailto:rietveld_l%40ill.fr";>rietveld_l...@ill.fr</a><br>
Subject: Re: [sdpd] Re: Are restraints as good as observations ?<br>
<br>
>What information capacity ? The fact is that imposing the expected <br>
>values you obtain a similar fit. This tells you that you cannot <br>
>discuss your unrestrained "information", because it is unreliable.<br>
> Information is something you may discuss reliably.<br>
> The only possible discussion about P3-O14 = 1.72(3)A is to say that <br>
>it is very probably strongly overestimated.<br>
<br>
After THIS unrestrained refinement one CAN discuss RELIABLY ALL interatomic distances including P-O, K-O, K-P, K-K and P-P, as well as angles, orientations etc., WITHIN THEIR UNCERTAINTIES that are also estimated RELIABLY according to the EXPERIMENTALLY DETERMINED deviations of the unrestrained P-O distances. After the restrained refinement NOTHING can be discussed RELIABLY since neither the values nor their uncertainties are determined EXPERIMENTALLY.<br>
After the unrestrained refinement one can state RELIABLY that the structure is DETERMINED with definite precision and, thus, discuss its features, compare it with other experimentally determined structures within their uncertainties, make more or less definite conclusions etc. After the restrained refinement one can only state that a hypothetical structure model is proposed and NOTHING can be concluded or discussed RELIABLY.<br>
Don't you see the difference??!!<br>
Determination = reliable experimental evaluation + reliable estimation of uncertainties.<br>
Now I probably understand your "colleagues".<br>
<br>
*******************************************************<br>
Leonid A. Solovyov<br>
Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia <a href="http://sites.google.com/site/solovyovleonid";>http://sites.google.com/site/solovyovleonid</a><br>
*******************************************************<br>
<br>
________________________________<br>
From: Armel Le Bail <<a href="mailto:xtal%40noos.fr";>xtal...@noos.fr</a>><br>
To: <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a><br>
Cc: <a href="mailto:rietveld_l%40ill.fr";>rietveld_l...@ill.fr</a><br>
Sent: Friday, August 2, 2013 12:40 AM<br>
Subject: Re: [sdpd] Re: Are restraints as good as observations ?<br>
<br>
<br>
> All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts.<br>
> <br>
> So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints.<br>
<br>
What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained "information", because it is unreliable.<br>
<br>
Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated.<br>
<br>
Such are powder results for complex cases.<br>
<br>
Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant.<br>
<br>
Best<br>
<br>
Armel <br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
------------------------------------<br>
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