Dear Prof. Fan, I do not think that this is a neccesarely an incommensurable structure. A lot of structures have translational NCS close to a translational that would make the space group higher and/or the primitive cell smaller. If one has C2221 and one destroys the centring operation x,y+1/2,z+1/2 by introducing a small perturbation, one just has pseudo symmetry/pseudo centring. If the data is processed in P212121, there need not be satelite reflections. If one wrongly assumes the sg to be C2221, there are 'satelite' reflections: the systematic absences due to the imperfect lattice translation (x,y+1/2,z+1/2). HTH Peter
> It seems to me that you are solving an incommensurately modulated > structure,since the pseudo-translation vector t = 0a + 0.47b + > 0.5c having the b > component equal to 0.47 and not exactly 0.5. There should be satellite > reflections which are NOT on nodes of the reciprocal lattice you have > chosen. If you try to solve an incommensurately modulated > structure by > rejecting satellites, what you get will be the “averaged > structure” and > not the true structure. In this case R factors should considerably > higherthan that of normal cases. More details about solving > incommensuratelymodulated structures can be found on the Webpage: > > http://cryst.iphy.ac.cn <http://cryst.iphy.ac.cn/> > > > > Hai-fu > > > > -- > > Professor Fan, Hai-fu > > Institute of Physics > > Chinese Academy of Sciences > > Beijing 100080, P.R. China > > > > Email: [EMAIL PROTECTED] > > URL: http://cryst.iphy.ac.cn <http://cryst.iphy.ac.cn/> > > > > > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf > Of Peter > J Stogios > Sent: 2007年3月25日 4:52 > To: [email protected] > Subject: [ccp4bb] Solving a structure by MR with a pseudo- > translation vector > > > > Hello, > > > > I posted a message about this a month ago and thanks to everyone > for > > their responses. At the time, I did not fully appreciate the > problem > > I was dealing with so this time my question is much more specific. > I > > would very much appreciate your help as this structure is turning > out > > to be very difficult to solve! > > > > I am trying to solve a structure by MR that should be easy, given > > that I have solved multiple structures of homologous proteins by > the > > same means. This crystal is 2.6 angstrom, apparently P212121, > with > > two molecules in the asymmetric unit that are related by the > pseudo- > > translation vector (0, 0.47, 0.5). This vector was identified > from > > the Patterson map, it is a peak 45% the height of the origin peak. > > > > As well, I have looked at all the reflection parity groups. Based > on > > I/sigmaI values output by Truncate, the k+l = 2n reflections are > as > > high as 2-fold greater in I/sigI vs. k+l = 2n+1 reflections from > 16 > > to 5.1 angstrom. From 5.1 to 2.9 angstrom, the reverse is true: > the k > > +l = 2n reflections are as high as 0.62-fold LOWER in I/sigI vs. > k+l > > = 2n+1. Then, from 2.9 to 2.6 angstrom, each reflection class is > > approximately equal in intensity. > > > > MR using Molrep's multi-copy search, using all reflections, > > consistently reproduces the pseudo-translation vector as the dyad > > vector between the two molecules. However, these solutions are > not > > easily noticeable (Molrep just picks the highest score but this > score > > does not stick out from the pack), and these solutions do not > refine > > well via rigid body or restrained refinement in Refmac. > > > > I have found some papers that show successful structure > > determinations by MR with pseudo-translation, but I am not sure > which > > approach to take to solve my structure. Do I need to remove the > > pseudo-weak or pseudo-strong reflections? Or do I actually use > the > > pseudo-weak or pseudo-strong reflections for the MR since they > will > > contain the information from the pseudo-translation? Which > > reflections should I refine against? Should I reindex to C222 to > > reflect the pseudo-face centering from the (0, 0.47, 0.5) vector? > Or > > am I missing something completely? > > > > Any help would be very very much appreciated!!!! Thanks! > > > > > > Peter > > > > > > ~ > > Peter J Stogios > > Ph.D. candidate, Privé Lab > > Dept. of Medical Biophysics, University of Toronto > > Toronto Medical Discoveries Tower (TMDT) at MaRS > > 101 College St., Rm. 4-308 > > Toronto, Ontario M5G 1L7 > > > > e: [EMAIL PROTECTED] > > w: http://xtal.uhnres.utoronto.ca/prive > > p: (416) 581-7543 > >
