You may well have a rhombohedral obverse/reverse twin. See Acta Cryst. B58 (2002) 477-481.
George On Tue, Jun 14, 2011 at 03:07:40PM -0400, Edward A. Berry wrote: > I'm currently struggling with what I think is a variation on this theme, > would appreciate comments as to whether my thinking is reasonable. > The space group is basically rhombohedral, but along the lines of spots > in the (hexagonal)L direction, with some crystals there are two weak > spots between each pair of indexed spots, and denzo tends to index these > crystals with a hexagonal lattice whose primitive cell is the same as > the hexagonal setting of the rhombohedral space group. > > There is a 2-fold operator (or perfect twin operator) perpendicular > to the 3-fold, so the hexagonal data can be indexed as P321 or H32 > (R32 in denzo?). Molecular replacement with one small domain seems > to work in P3(1)21 or H32. but no density shows up outside the > search model so I'm not sure. > > If indexed in P321, Xtriage finds native patterson peaks: > x y z height p-value(height) > ( 0.332,-0.335, 0.333 ) : 73.464 (1.830e-06) > ( 0.282,-0.440, 0.345 ) : 5.416 (8.402e-01) > > The first of which vaguely resembles the translational operators in H32: > 155 18 6 H32 PG321 TRIGONAL 'H 3 2' > X,Y,Z > 2/3+X,1/3+Y,1/3+Z > 1/3+X,2/3+Y,2/3+Z > > So could this be a case of rhombohedral symmetry breaking down into > trigonal? > > eab > > herman.schreu...@sanofi-aventis.com wrote: > >Dear Konstatin, > > > >First I would reiterate what Fred has said: you only know the space > >group once the structure has been solved and completely refined. > >Especially bad maps and unsuccesful molecular replacements may point to > >a wrong space group assignment. > > > >Second, what causes strong and weak reflections? I once worked it out > >for a case where only one axis was doubled, but I guess that in your > >case it might be similar: for the small unit cell, your crystal may look > >like AAAAAAAAA (all layers of A's, unit cell is A). In case of the > >doubled unit cell, the crystal will look like ABABABABAB (alternating > >layers of A and B's, unit cell AB). If A is identical to B, the > >scattering of the A's will cancel the scattering of the B's for the odd > >reflections and you have the small unit cell. If the A's are a little > >different from the B's, your even reflections will have the sum of the > >scattering of A and B, and the odd reflections will have the difference. > >So if the odd reflections are weak, this means that the differences > >between the A and B layers are small and you could consider to ignore > >them for a preliminary structure, keeping in mind that the resulting > >electron density will be the sum (superposition) of the densities of the > >A and B layers. You might get clashes, since the differences in A and B > >layers may be caused by the crystal packing so I would increase the > >allowed number of clashes e.g. in Phaser. Once you have the small unit > >cell, you could try to figure out how the big unit cell may look like. > >Your situation might be different, but I would definitively try it. > > > >Herman > > > >-----Original Message----- > >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > >Marco Lolicato > >Sent: Monday, June 13, 2011 5:16 PM > >To: CCP4BB@JISCMAIL.AC.UK > >Subject: Re: [ccp4bb] XDS question > > > >Thank you to all! > > > >@Frederic > >> > >>I have a problem with the following sentence: > >>"if I collect all spots I get good map, but it is impossible to solve > >the structure by molecular replacement" - if you have a good map (I > >assume electron density map) then the structure is solved... for me a > >good map is a map I can interpret. > > > >You're right, I said "good map" instead of "good output values". > > > > > >@Konstantin > >> > >>It is possible to process diffraction spots from both crystals using > >>XDS. The procedure is described here (under 'Index and integrate > >>multiple-crystal diffraction'): > >>http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Tips_and_Tr > >>icks > > > >I tried but with no success! :( > > > > > >@Kay and all the others > > > >The following links are the images: > > > >http://www.facebook.com/photo.php?fbid=2127189780277&set=o.1363238963856 > >79&type=1&theater > > > >http://www.facebook.com/photo.php?fbid=2127189180262&set=o.1363238963856 > >79&type=1&theater > > > >http://www.facebook.com/photo.php?fbid=2127188820253&set=o.1363238963856 > >79&type=1&theater > > > > > > > > > >...then a little bit more details... > >so, if I process only the strong spots I have those cell parameters: > > a=b=96.66 c=112.26 alpha=beta=gamma= 90 > > > >f I process all the spots I have those cell parameters: > > a=b=216.4 c=112.4 alpha=beta=gamma= 90 > > > >In both cases the space group is I422. > > > > > >Thank you again to all, do you have any other suggestion? > > > > > >Marco > > > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
