Hmm - why should a translational peak not be along the 40 axis? Anyway othercell shows this Conversion of cell 40, 32, 101, 90, 101, 90
can give Laue groups C m m m 40.0 198.3 32.0 90.0 90.0 89.6 0.42 [h,h+2l,-k] Possible spacegroups: <C 2 2 21> <C 2 2 2> or C 1 2/m 1 40.0 198.3 32.0 90.0 90.0 89.6 0.42 [h,h+2l,-k] or C 1 2/m 1 198.3 40.0 32.0 90.0 90.0 90.4 0.42 [-h-2l,h,-k] or P 1 2/m 1 40.0 32.0 101.3 90.0 101.8 90.0 0.84 [-h,-k,h+l] That is so close to your input cell that twinning is a very likely option. What does thedata processing suggest - look at pointless or Xtriage or something Eleanor On 15 November 2013 18:18, Niu Tou <niutou2...@gmail.com> wrote: > It may be helpful to add some information during index. HKL2000 could find > four reasonable solutions: > 40, 32, 101, 90, 101, 90 for P1 and P2 > 200, 40, 32, 90, 90, 90 for C2 and C222 > > It looks very strange to me since these two unit cells look differently, but > during refinement the predicated spots are identical, and they produced > similar quality data--at least from those output > parameters. > > All solutions (including P21, C2221) have the 95% off origin peak and > several minor ones. The 95% peak is at (0.5 0 0) on the 40 line, so if cut > it into half, that dimension will be too small (20 only). HKL2000 also did > not give any solution with one dimension as 20. > > Maybe I did not get a right index yet, I wonder any expert can tell > something from these information? > > > On Fri, Nov 15, 2013 at 6:41 AM, Melanie Vollmar > <melanie.voll...@sgc.ox.ac.uk> wrote: >> >> Dear Niu, >> >> I had an interesting pseudo-translation case recently where my off-origin >> peak was located near the centre of the unit cell (fractions a=0.5, b=0.46, >> c=0.5) of a P222 symmetry. Processing and phasing in P222 looked reasonable >> and the model could be built. I had background density which I thought of as >> water. I got suspicious when I identified density for a helix which was near >> my build main chain but could not be joined and built or be accounted for by >> looking at symmetry mates. Moreover I got stuck in refinement with R/Rfree >> 25/30%. I could identify which part of the protein caused me the trouble on >> crystal packing and the appearance of the off-origin peak. In my case it was >> the C terminus. So I used a new construct with swapped purification tag (N >> to C terminus). This altered the peptide sequence for the C terminus and >> allowed the protein to pack nicely into I222. This turned my off-origin peak >> into a true symmetry operator. >> >> I also had reasonable processing and phasing results for P2 and C2. >> >> So besides the strength of your off-origin peak it may be off some use to >> look at the location. >> >> HTH >> >> Melanie >> ________________________________ >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou >> [niutou2...@gmail.com] >> Sent: 14 November 2013 23:58 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Weird MR result >> >> 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 >>>> >>>> >>> >> >
