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Tutorials and Examples

Platon (Shelx Compatible) Structure Analysis Toolkit Software by Ton Spek

An example of why Platon/Addsym should be considered a mandatory program for all crystallographers

(re: Short Communication: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh)

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Platon's Addsym Manual - by Ton Spek


The Addsym function within Platon should be considered a mandatory tool for any small molecule crystallographer and powder diffractionist involved in solving and refining crystal structures. Addsym "(building on Yvon LePage's powerful published MISSYM (C) algorithm)" allows the identification of missed symmetry; which minimizes the chances of publishing structures in the wrong spacegroup. It can also identify miss-fitting atoms for the benefit of the crystallographer who can then check if these are legitimately breaking a possible better symmetry. Addsym is "also" applicable to inorganic structures, mineral structures and structures solved and refined using powder diffraction methods.

Platon makes this type of check quite trivial and easy to do for all structures: just run Platon for UNIX or Windows and open either a CIF, Shelx or Platon file. More compelling reasons for routinely do this are in the following webpage on "Cases of Pseudo Symmetry or real missed Symmetry in the CSD".


In this example, we will be concentrating on the example based on the "Short Communication", Acta Cryst B56 (2000) 744 from Richard E. Marsh.

The NIXQAM structure was originally published as triclinic with a spacegroup of P1, reinterpreted by Richard Marsh as monoclinic with spacegroup of C2, then shown by Platon Addsym to be Orthorhombic with spacegroup of Fdd2.

Short Communication Abstract: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh

Synopsis: The space group of bis((phenyl-O,N,N-azoxy)oxy)methane, previously revised from P1 to C2, is further revised to Fdd2.

Abstract: The structure of bis((phenyl-O,N,N-azoxy)oxy)methane. C13H12N4O4, originally reported as triclinic, space group P1 [Zyuzin et al. (1997). Isz. Akad. Nauk SSSR Ser. Khim. pp. 1486-1492; CSD recode NIXQAM] was recently revised to monoclinic, space group C2 [Marsh (1999)]. Acta Cryst. B55, 931-936]. It is properly described as orthorhombic, space group Fdd2.

Extracts from the short communication:

"While the deviations of these angles from 90 are somewhat greater than the reported precision estimates of ~0.07 (Zyuzin et al., 1997), they are not out of line with the accuracies that are often encountered (Taylor & Kennard, 1986; Marsh, 1995)."

"Perhaps a word of caution is in order: there may be danger in assuming that the symmetry of a reported structure should be revised without access to the basic experimental data. However, the danger seems minimal in the present case, where the reported structure conforms to the higher symmetry within such small deviations; since the structure obeys the symmetry of Fdd2" (Laue group, mmm, the original data must do the same. Where examination of the original data - particularly the very weak reflections - may be vitally important is in cases involving the ambiguity between a centrosymmetric and a noncentrosymmetric strutcure within the same Laue group, since seemingly important distortions from centrosymmetry may be reflected in only minimal changes in all but the very weakest diffractin intensitiess."


Downloadable structure files

The relevant Cambridge structure Database files can be downloaded below:


If running Platon for UNIX, just type platon filename.ins, platon filename.res or platon filename.cif to enter the Shelx or CIF file.

For Platon for Windows, open a structure file using the File, Open command then select Platon, PLATON Menu to view the common platon menu options.

Platon Menu Window


Selecting PLUTONauto will allow you to view and manipulate the structure.

Following is the P1 triclinic structure viewed in the Pluton mode of Platon.

Triclinic structure in viewed in Pluton mode


Following is the C2 monoclinic structure viewed in the Pluton mode of Platon.

Triclinic structure in viewed in Pluton mode


Load the original Triclinic structure in Platon. Select ADDSYM (under Symmetry) and hang back and let Platon do the rest. In this case, Platon has found the extra symmetry and is suggesting the orthorhombic Fdd2 is a better spacegroup for this structure.

Addsym finished running


The results are in the "Platon Dialog Window", examine then and determine for yourself if Platon is onto something. There is move voluminous output if you wish to examine this.

Addsym Output in the Dialog Window


If you instead run Addsym-PLT, a structural output will be generated to the screen. Or the resulting structure can be outputted directly to a Shelx *.res file using the ADDSYM-SHX menu option.

Addsym-PLT graphical structure output Window


Pluton can also give packing diagrams very easily using the pack range option.

Addsym-PLT graphical structure output Window


[Tutorials page] | [Platon Tutorial Index]
[Platon Introduction] | [Obtaining Platon] | [Installing and Running Platon]
[Starting out with Platon] | [Platon Runthroughs] | [Platon's Addsym]

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