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[sdpd] Re: Unrestrained SDPD future
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- Subject: [sdpd] Re: Unrestrained SDPD future
- From: "armellebail" <xtal...@noos.fr>
- Date: Thu, 22 Aug 2013 13:56:09 -0000
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<p>Hi Leonid,<br>
<br>
Thanks for confirming all my structures (at least the non-H atoms).<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>
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>
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>
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>
</p>
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