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Re: [sdpd] Re: Are restraints as good as observations ?
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<p><br>
> >The problem of having jammed the wrong molecule<br>
> > into a unit cell can be identified by restraints which<br>
> > are violated. With rigid bodies it is more difficult to<br>
> > find out what the data are trying to tell you. Is this<br>
> >wrong molecule issue the problem you fear?<br>
><br>
>I prefer resolving such problems by unrestrained refinement with minimal <br>
>rigid constraints on unambiguous parts which can't be refined.<br>
<br>
All Rietvelders (included me) are certainly trying a completely free <br>
refinement before to decide or not to use selected restraints. I tried, and <br>
finally preferred to use some soft restraints (the fear of being DFTized <br>
because of some interatomic distances obviously out of their usual range). <br>
Some of my old SDPDs without restraints were DFTized, the DFTizers were <br>
claiming that powder results are good for some dustbin... Now I am guilty <br>
according to Leonid (guilty to not use DDM working so much better than <br>
Fullprof in such cases; dur to the so clever background treatment)... But <br>
the paper was accepted ;-). A few days after I received a DFTization... Am <br>
I especially scrutinized ? I feel more and more uncomfortable about such <br>
verifications of everything I do (Leonid, I suggest you to try K4P2O7 - <br>
synchrotron data, space group P61 - for which I had to put distance <br>
restraints on the three P2O7 independent groups - Powder Diffraction, 28, <br>
2-12, 2013) !<br>
<br>
Are all my results so bad ? Below is the COMPSTRU Bilbao software output of <br>
the comparison of the calcium glycinate trihydrate as published in Acta C <br>
and as from the Leonid DDMization with contraints "only" on H atoms (a lot <br>
of constraints BTW, there are 14 independent H atoms...). The measure of <br>
similarity is 0.027. We will have to wait for the single crystal results <br>
(if any some day) before to conclude to the best way to proceed in that <br>
case. Anyway, if the molecule is wrong, it is wrong in both powder refinements.<br>
<br>
Armel<br>
<br>
COMPSTRU results :<br>
<a href="http://www.cryst.ehu.es/cryst/compstru.html";>http://www.cryst.ehu.es/cryst/compstru.html</a><br>
<br>
WPAtomAtomic Displacements<br>
uxuyuz|u|<br>
2i(x,y,z)Ca1 0.0036 -0.0003 -0.0036 0.0367<br>
2i(x,y,z)OW1 -0.0028 -0.0017 0.0034 0.0322<br>
2i(x,y,z)H11 -0.0224 -0.0093 0.0195 0.2275<br>
2i(x,y,z)H12 -0.0187 0.0023 0.0031 0.1817<br>
2i(x,y,z)OW2 -0.0043 -0.0022 0.0122 0.0749<br>
2i(x,y,z)H21 0.0135 0.0121 -0.0153 0.1720<br>
2i(x,y,z)H22 0.0078 0.0099 -0.0259 0.1747<br>
2i(x,y,z)OW3 -0.0025 0.0040 0.0046 0.0522<br>
2i(x,y,z)H31 -0.0025 0.0040 0.0045 0.0519<br>
2i(x,y,z)H32 -0.0025 0.0040 0.0045 0.0519<br>
2i(x,y,z)N1 -0.0017 -0.0072 0.0149 0.1082<br>
2i(x,y,z)H41 0.0032 0.0076 0.0178 0.1326<br>
2i(x,y,z)H42 0.0009 0.0027 0.0269 0.1589<br>
2i(x,y,z)N2 0.0090 0.0011 -0.0302 0.1759<br>
2i(x,y,z)H51 0.0190 0.0038 -0.0417 0.2671<br>
2i(x,y,z)H52 0.0234 0.0034 -0.0400 0.2830<br>
2i(x,y,z)O1 0.0008 -0.0016 -0.0112 0.0652<br>
2i(x,y,z)O2 0.0037 -0.0009 0.0073 0.0623<br>
2i(x,y,z)O3 0.0001 0.0026 -0.0066 0.0456<br>
2i(x,y,z)O4 0.0044 0.0095 0.0041 0.1011<br>
2i(x,y,z)C1 -0.0115 -0.0074 0.0074 0.1231<br>
2i(x,y,z)H61 -0.0116 -0.0080 0.0022 0.1259<br>
2i(x,y,z)H62 -0.0035 -0.0037 0.0091 0.0641<br>
2i(x,y,z)C2 -0.0149 0.0039 0.0074 0.1502<br>
2i(x,y,z)C3 -0.0037 0.0067 -0.0093 0.0995<br>
2i(x,y,z)H71 -0.0188 0.0092 0.0111 0.2094<br>
2i(x,y,z)H72 0.0083 0.0278 -0.0174 0.2834<br>
2i(x,y,z)C4 0.0085 -0.0129 -0.0108 0.1626<br>
<br>
NOTE: ux, uy and uz are given in relative units. |u| is the absolute <br>
distance given in Å<br>
<br>
Evaluation of the structure similarity<br>
<br>
Sdmax. (Å)dav. (Å)?<br>
0.00040.28340.04030.027<br>
<br>
* Lattice and atomic position criteria:<br>
<br>
* The <nph-doc-compstru.htm>degree of lattice distortion <br>
(S<nph-doc-compstru.htm>) is the spontaneous strain (sum of the squared <br>
eigenvalues of the strain tensor divided by 3). For the given two <br>
structures, the degree of lattice distortion (S) is 0.0004.<br>
* The maximum distance (dmax.) shows the maximal displacement <br>
between the atomic positions of the paired atoms. The maximum distance <br>
(dmax.) in this case is: 0.2834 Å<br>
<br>
* The <nph-doc-compstru.htm>average distance <br>
(dav.<nph-doc-compstru.htm>) is defined as the average over the primitive <br>
unit cell of the distances between the atomic positions of the paired <br>
atoms. For this case the average distance (dav) is calculated as 0.0403 Å.<br>
* The <nph-doc-compstru.htm>measure of similarity <br>
(?<nph-doc-compstru.htm>) (Bergerhoff et al., 1998) is a function of the <br>
differences in atomic positions (weighted by the multiplicities of the <br>
sites) and the ratios of the corresponding lattice parameters of the <br>
structures. The measure of similarity (?) calculated for this case is 0.027.<br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
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