The 95% off-origin peak in the Patterson might be telling you that the true space group has a centering operation that was missed, or the cell was doubled, in the indexing step (i.e. systematically absent spots are being indexed and integrated). If the zeros for systematically absent spots are replaced by noise, the origin-equivalent peak that should come up at 100% in the native Patterson can be reduced by something like 5%. Alternatively, you may have something extremely close to a centering operation, but not exactly crystallographic. To choose between these, you need to look at the original diffraction images to see whether there really are spots in the places that would be predicted to be absent if there were an exact centering operator or if the cell were half as long.
Either way, you could probably get away with temporarily treating the translation corresponding to the Patterson peak as an exact crystallographic translation, process the data in the corresponding space group (which, at least, xtriage will tell you and maybe also pointless), and solve the molecular replacement problem in that space group. If you get a clear solution, then if the translation is non-crystallographic, you can worry later about how the exact symmetry is broken in the crystal. However, if the approach of using a smaller cell would work, I'm surprised that recent versions of Phaser that account for translational NCS would not also work. If you looked for two copies in one search, Phaser should have accounted for the tNCS implied by the Patterson peak. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 14 Nov 2013, at 23:58, Niu Tou <niutou2...@gmail.com> wrote: > Dear Phil, > > I used PHASER to do the task. I have double checked and both files have the > same prefix, so they are from the same output. I have also checked the > headers again, they have the same spacegroup. Actually I was trying to search > for two different molecules but only one was found. The spacegeoup is P2 and > I am quite sure it is not P21 from system absence. > > One possibility is that the space group was wrong, since there is a 95% off > origin peak. There are several choices from data processing, P1, P2, C2 C222, > all have this large off origin peak. I wonder if this 95% peak can tell some > information? > > It will not surprise me if this result is incorrect, however how could these > regular density be? > > Best, > Niu > > > On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey <pjeff...@princeton.edu> wrote: > Hello Niu, > > 1. We need extra information. What program did you use ? What's the > similarity (e.g. % identity) of your model. What's your space group ? Did > you try ALL the space groups in your point group in ALL the permutations > (e.g. in primitive orthorhombic there are 8 possibilities). > > 1a. My best guess on limited info is that you've got a partial solution in > the wrong space group with only part of the molecules at their correct > position. > > 2. I recently had a very unusual case where I could solve a structure in > EITHER P41212 or P43212 with similar statistics, but that I would see > interpenetrating electron density for a second, partial occupancy molecule no > matter which of these space groups I tried (and it showed this when I > expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin, in > retrospect, but we obtained a more friendly crystal form. I hope you don't > have something like that, but it's possible. > > Phil Jeffrey > Princeton > > > On 11/14/13 5:22 PM, Niu Tou wrote: > Dear All, > > I have a strange MR case which do not know how to interpret, I wonder if > any one had similar experiences. > > The output model does not fit into the map at all, as shown in picture > 1, however the map still looks good in part regions. From picture 2 we > can see even clear alpha helix. I guess this could not be due to some > random density, and I have tried to do MR with a irrelevant model > without producing such kind of regular secondary structure. > > This data has a long c axis, and in most parts the density are still not > interpretable. I do not know if this is a good starting point. Could any > one give some suggestions? Many thanks! > > Best, > Niu > > > >
