Thanks for the input on SUPERFLIP. I didn’t know that it had such symmetry
search capabilities, and I will certainly look into it.

For everybody’s 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 Jacco’s 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 I’m 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 I’m doing wrong or point out
> > something I can read. I’m aware of the Platon/Addsym resources on the
> > ccp14, but I didn’t 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:
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> 
> 




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