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