Different atomic coordinates
Dear All, I am trying to refine a phase that has a structure analogue with different chemical composition. The problem is that using the published atomic coordinates one cannot get a proper refinement (mismatch in the diffraction intensities). When I process the data and solve the structure by direct methods I get atomic coordinates that are suitable for a good a Rietveld refinement (the structure is the same). If somebody has explanation of this problem I will be very grateful to hear it. Many thanks in advance. Stanislav
Re: Different atomic coordinates
Stanislav Ferdov wrote: Dear All, I am trying to refine a phase that has a structure analogue with different chemical composition. The problem is that using the published atomic coordinates one cannot get a proper refinement (mismatch in the diffraction intensities). When I process the data and solve the structure by direct methods I get atomic coordinates that are suitable for a good a Rietveld refinement (the structure is the same). If somebody has explanation of this problem I will be very grateful to hear it. Many thanks in advance. You really should give some details. Does the space group have two possible origins? Etc, etc Larry
Re: Different atomic coordinates
Dear Stanislav, Depending on the program you are using to perform the refinement and the particular space group of your structure, it could happen that the coordinates you got from the database refer to a different origin of the coordinate system than the coordinates you got from the structure determination. In many censtrosymmetric space groups the highest symmetry point in the cell have no -1 (center of symmetry), the convention used to place the origin of the cell in this highest symmetry point, however most of the refinement and solution programs will assume the origin is on the highest symmetry point of the cell containing a center of symmetry (no matter if there is a higher symmetry point) because it simplifies computations, etc. This discrepancy in origin choice could account for your problem. This happens very frequently with quartz where two sets of coordinates are stored in databases referring to two possible origins of the unit cells not always given with the coordinates, producing confussion. Check if your space group got two alternative origins (for most centrosymmetric space groups with the highest symmetry point not containing a center of symmetry both descriptions are given in the International Tables with alternative choices) I hope this helps, Good luck Leo Prof. Dr. Leopoldo Suescun Cryssmat-Lab/DETEMA/Facultad de Quimica Universidad de la Republica Montevideo, Uruguay
Re: Different atomic coordinates
it could happen that the coordinates you got from the database refer to a different origin... Databases simply store the results of earlier determinations, for which the symmetry setting and coordinates should be coherent. It is not unknown for errors to occur, but commercial small structure databases ICSD and CSD are carefully checked, as are CIFs published in journals such as Acta Cryst. The easiest and most powerful check for a fundamental error in the structure description is to actually draw it on your computer - most mistakes, such as wrong origin, will be immediately apparent. Both ICSD and CSD allow you to draw structures. That's the first thing to do. BTW ICSD-Web http://icsdweb.fiz-karlsruhe.de/ will now draw anisotropic vibration amplitudes (also coming soon to Acta Cryst on-line). This is a good test for systematic errors in data and structure refinements, as is the calculation of bond-lengths and angles. Alan __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE [EMAIL PROTECTED] +33.476.98.41.68 http://www.NeutronOptics.com/hewat __
Different atomic coordinates
Dear All, thank you very much for your comments. In fact my material is hexagonal. A study on the systematic absences did not allow a unique assignment of the space group and six possible solutions were determined: P63mc (No. 186), P-62c (No. 190), P63/mmc (No. 194), P3c1 (No. 158) and P-31c (No. 163). I tried to solve the structure in all these space groups but the only successful solution appeared in P63mc (No. 186). The structure can be drawn and all atomic distances and angles look ok. Stanislav
