Thanks for the input on SUPERFLIP. I didnt know that it had such symmetry search capabilities, and I will certainly look into it.
For everybodys information, William Bisson has kindly run my test on the latest unix version of Platon and he gets the same result as me. I will follow Jaccos advice and email Ton Spek directly. Thanks again for you input! Magnus > -----Opprinnelig melding----- > Fra: Van der Lee [mailto:[EMAIL PROTECTED] > Sendt: 24. juli 2008 17:28 > Til: rietveld_l@ill.fr > Kopi: "Magnus H. Sørby" > Emne: Re: Addsym trouble > > Hi Magnus and others, > > I do not know about the troubles with PLATON, but I used this case for a > test using the symmetry determination method implemented in SUPERFLIP. > > Magnus' first test structure gives in SUPERFLIP (use the 'perform > symmetry' option with a manually generated CIF-file) P21/m as does PLATON. > > Interesting is that SUPERFLIP's logfile gives an indication how good or > wrong symmetry elements are with respect to the electronic density. This > is called the 'symmetry agreement factor' (phi_sym). If phi_sym=0 then > the density is perfectly symmetrical with respect to the symmetry > operator. If phi_sym=1.0 then the density is completely random with > respect to the symmetry operator. > > For the first test structure phi_sym is situated in between 0.35 and > 0.70 for the non-trivial symmetry operators in Cmcm. Is this sufficient > to consider that the operators are present? No, but they are indeed in > the 'grey' area between present and non-present, which we call 'pseudo'. > > SUPERFLIP determines Pbnm for Magnus' second structure, with again quite > a number of symops in the grey area between 0.37 and 0.58. The third > structure gives also Pbnm, but now with 'grey' phi_sym values between > 0.26 and 0.51 (the c-glide being at 0.26). Note that the SUPERFLIP > threshold for including a symop is set at 0.25. > > Note that the C-centering is not detected by SUPERFLIP, although it > should do so if the atoms are placed at the ideal positions. This is > probably a bug. > > The interesting point about the SUPERFLIP approach is, which is by the > way fundamentally different from the PLATON approach, that the notion > 'pseudo' can now be quantified. > > best wishes, Arie > > > Magnus H. Sørby wrote the following on 23/07/2008 17:31: > > Hi! > > > > > > > > I was getting some unexpected results from Addsym (Platon version > > 230608) so I ran some tests to try to clear things up. Now Im confused > > to the point where I need help! > > > > > > > > The test structure I have used is: > > > > Space group P-1 > > > > a = 3.5 Å b = 12.3 Å c = 4.5 alpha = beta = gamma = 90 deg > > > > > > > > Al1 in 0.06 0.85 0.75 > > > > Al2 in 0.49 0.33 0.77 > > > > > > > > This is pseudo-/Cmcm/ symmetry. True /Cmcm/ positions (0 x ¾ , ½ x ¾) > > are only 0.24 Å away. > > > > > > > > There are three points that are about to drive me nuts: > > > > > > > > 1) Addsym suggests /P2_1 /m/ instead of /Cmcm/. It has no effect to > > increase the criteria parameters d1, d2 and d3 from the default 0.25 Å > > to 0.5 Å. > > > > > > > > 2) If I move the structure somewhat closer to /Cmcm /symmetry by putting > > Al1 in, say, 0.03 0.85 0.75, I get no new space group suggestion at > > all! Addsym produces some lines that say > > > > > > > > E: SYMM TRANSLATION n/a: 0.958 .500 0 > > > > > > > > during the run and writes > > > > > > > > Higher (pseudo)symmetry not compatible,(current symmetry retained) > > > > > > > > in the lis-file. > > > > > > > > 3) When I move the atoms very close to the Cmcm positions, e.g. > > > > > > > > Al1 in 0.01 0.84 0.75 > > > > Al2 in 0.49 0.33 0.74 > > > > > > > > then Addsym suggests /Cmcm/ if I launch it from the command line. If I > > use the graphical interface, it suggests /Pmma/ instead. That happens > > even if I place the atoms in ideal /Cmcm/ positions. > > > > > > > > Are these things user errors or bugs? If they are user errors I would be > > very grateful if anybody could explain what Im doing wrong or point out > > something I can read. Im aware of the Platon/Addsym resources on the > > ccp14, but I didnt find anything there that helped me. > > > > > > > > I see on the Platon web page that the newest version should be from July > > 13 2008, but the version I can download is still from June. > > > > > > > > Best wishes, > > > > Magnus > > > > > -- > ************************************************************************** > * > A. van der Lee > Institut Européen des Membranes > CNRS - UMR 5635 > Université de Montpellier II - Case Courrier 047 > Place E. Bataillon > 34095 MONTPELLIER Cedex 5 - FRANCE > > Tel : 33 (0) 4 67 14 91 35 > Fax : 33 (0) 4 67 14 91 19 > > Website X-ray scattering facility ICG/IEM: > http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html > ************************************************************************** > ** > >
