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[sdpd] Re: Unrestrained SDPD future
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- Subject: [sdpd] Re: Unrestrained SDPD future
- From: "L_Solovyov" <l_solovyov...@yahoo.com>
- Date: Fri, 23 Aug 2013 06:10:59 -0000
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<p>>So, the conclusion is that either I am a poor FULLPROF user or I<br>
>should abandon it for DDM (I guess you wanted me to tell that since<br>
>the beginning ?), the latter option implying that FULLPROF is a bad<br>
>Rietveld software.<br>
<br>
Rapid-fire conclusions and emotions instead of careful analysis again...<br>
<br>
As I noted earlier, the alternative is in a more accurate approach to the experiment and the modeling instead of compensating the inaccuracy by restraints. <br>
To achieve the reasonable geometry for that cobalt compound the following things were done beside DDM:<br>
>For both the main and the admixture hemihydrate phases<br>
>the strain anisotropic broadening and the preferred orientation<br>
>ellipsoid were refined. A more accurate model of the admixture<br>
>hemihydrate phase was chosen. The low-angle interval<br>
>was excluded as being, most likely, affected by the<br>
>primary-beam overspill. An additional micro-admixture has<br>
>been identified whose inclusion into the model resulted in<br>
>further notable improvements of the structure geometry.<br>
<br>
If one ignores all these peculiarities and chooses a simplified model (as you did) one will have those "crazy" distances and angles both in Fullprof and in DDM.<br>
The principal advantages of DDM before Fullprof are in the baseline treatment, the weighting scheme and the estimation of uncertainties.<br>
<br>
>Possibly, the question if a lambda DDM user<br>
>would obtain similar results as the<br>
>software author should have an answer too?<br>
<br>
I'm sure that other DDM users have all chances to obtain even better results since my refinement was rather cursory (3 hours with 2 coffee breaks).<br>
<br>
>And we still wait for your performance on the protein<br>
>or do you finally admit that restraints should be used sometimes?<br>
<br>
I have neither expertise nor motivation for entering the field of protein SDPD. Regarding the inevitability of restraints there, I may refer to the Guidelines you mentioned: "(viii) As an alternative to geometric restraints (which increase the number of observations), try using rigid-body descriptions (which reduce the number of parameters)." <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>, "armellebail" <xtal...@...> wrote:<br>
><br>
> Hi Leonid,<br>
> <br>
> Thanks for confirming all my structures (at least the non-H atoms).<br>
> <br>
> <br>
> > Characteristic distances and their expectations:<br>
> > Pos. Â Â Dist. Â Exp.<br>
> > Co-O1 Â 1.92(2) Â 1.91<br>
> > Co-O2 Â 1.94(2) Â 1.91<br>
> > Co-N1 Â 1.98(1) Â 1.96<br>
> > Co-N2 Â 1.95(2) Â 1.96<br>
> > Co-N3 Â 1.92(2) Â 1.96<br>
> > Co-N4 Â 1.99(1) Â 1.96<br>
> > C1-O1 Â 1.31(4) Â 1.32<br>
> > C1-O2 Â 1.34(4) Â 1.32<br>
> > C1-O3 Â 1.25(3) Â 1.23<br>
> > N5-O4 Â 1.27(3) Â 1.24<br>
> > N5-O5 Â 1.23(3) Â 1.24<br>
> > N5-O6 Â 1.25(3) Â 1.24<br>
> <br>
> <br>
> I must say that my results without restraints (using FULLPROF)<br>
> are quite different from your DDM ones for that cobalt compound <br>
> (and also for the others, the glycinate and K4P2O7) :<br>
> <br>
> Co1 O1 1.89(3) <br>
> Co1 O2 1.89(3) <br>
> Co1 N1 2.104(13) <br>
> Co1 N2 1.966(14) <br>
> Co1 N3 1.946(15) <br>
> Co1 N4 2.078(13) <br>
> C1 O1 1.39(4) <br>
> C1 O2 1.29(4) <br>
> C1 O3 1.19(4) <br>
> N5 O4 1.05(4) <br>
> N5 O5 1.23(4) <br>
> N5 O6 1.42(3) <br>
> <br>
> O1 C1 O2 97(3) <br>
> O1 C1 O3 116(4) <br>
> O2 C1 O3 137(4) <br>
> <br>
> O4 N5 O5 116(4) <br>
> O4 N5 O6 104(3) <br>
> O5 N5 O6 102(3) <br>
> <br>
> <br>
> Hard to publish that (IMHO), even if the R factors largely decreased <br>
> in all cases... Hence the restraints.<br>
> <br>
> So, the conclusion is that either I am a poor FULLPROF user or I <br>
> should abandon it for DDM (I guess you wanted me to tell that since<br>
> the beginning ?), the latter option implying that FULLPROF is a bad Rietveld software. I will not select between both possibilities.<br>
> <br>
> Other FULLPROF users may test the data by themselves quickly since<br>
> the FULLPROF .pcr and .dat files are included at the end of the CIF <br>
> which can be downloaded at the IUCr Acta E Website.<br>
> <a href="http://dx.doi.org/10.1107/S1600536813017522";>http://dx.doi.org/10.1107/S1600536813017522</a><br>
> They have just to remove the restraints (keep them on H atoms maybe),<br>
> and play up to attain the same results as with DDM, if possible.<br>
> <br>
> Possibly, the question if a lambda DDM user would obtain similar results as the software author should have an answer too ?<br>
> <br>
> And we still wait for your performance on the protein or do you finally admit that restraints should be used sometimes ?<br>
> <br>
> Best,<br>
> Armel<br>
> (back from vacations...)<br>
> <br>
> <br>
> PS recommending the lecture of another open paper, "Rietveld<br>
> refinement guidelines" where the word "restraints" occurs 12 times<br>
> <a href="http://journals.iucr.org/j/issues/1999/01/00/gl0561/index.html";>http://journals.iucr.org/j/issues/1999/01/00/gl0561/index.html</a><br>
> <br>
> § 12.8. The final structure is not chemically sensible<br>
> (impossible interatomic distances or displacement<br>
> factors)<br>
> (i) Try using restraints to keep interatomic distance<br>
> sensible and increase the weight of the restraints if<br>
> necessary. <br>
> <br>
> etc<br>
> <br>
> Seems that new Rietveld guidelines will be published soon by Leonid.<br>
><br>
<br>
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