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Yuan Cheng wrote: > Eleanor Dodson wrote: >> This phenonema doesnt necessarily mean you have lattice-tranlation >> defects - pseudo translations are quite common with perfectly good >> crystals. >> Lattice translation defects usually imply your "crystal" has two or >> more layered different crystals in the beam.. It can be best detected >> by an analysis of the data statistics. >> >> Eleanor >> >> >> Yuan Cheng wrote: >>> Eleanor Dodson wrote: >>>> You must have a pseudo translation vector of ~ 0.02 0.5 0.0 >>>> That relates solution 1 and 2, and 3 and 4. >>>> >>>> That makes it hard to determine space group - there will be >>>> absences along 0k0 because of the translation so the space group >>>> could be P 2i 2 2i or P2i 21 2i >>>> But which ever SG it is thedata with k odd will be weak, and that >>>> means you will have a higher R factor. >>>> >>>> Eleanor >>>> >>>> >>>> >>>> >>>> Jerry McCully wrote: >>>>> Dear all: >>>>> >>>>> I am currently refining a structure solved by MAD and >>>>> somehow the R factor got stuck around 30% with 2.2 resolution. >>>>> >>>>> There are four molecules in one ASU. Two had very good >>>>> density map and the other two were not equally good. >>>>> >>>>> I tried using NCS during refinement but it did not help >>>>> much. >>>>> >>>>> Then I checked my data. Actually I found that there are >>>>> alternate layers of strong and weak reflections. THe crystal is >>>>> in a thin-plate shape with orthorombic space group. >>>>> >>>>> Then I looked at my molecular replacement solution from Phaser >>>>> using my native data. >>>>> >>>>> Actually phaser gave two sets of solutions, which showed >>>>> slightly different positions. >>>>> >>>>> You can also see that there is a translation inside the same set >>>>> of solution. >>>>> >>>>> >>>>> SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0 >>>>> LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=46.1 PAK=0 >>>>> LLG=4045 >>>>> SOLU 6DIM ENSE ensemble1 EULER 184.052 0.185 175.770 FRAC >>>>> -0.49889 -0.00218 -0.00000 >>>>> SOLU 6DIM ENSE ensemble1 EULER 225.116 0.167 134.696 FRAC >>>>> -0.47056 0.49706 0.00051 >>>>> SOLU 6DIM ENSE ensemble1 EULER 359.333 31.677 180.633 FRAC >>>>> 0.75769 -0.71475 -0.14004 >>>>> SOLU 6DIM ENSE ensemble1 EULER 359.373 31.969 180.711 FRAC >>>>> 0.73074 -0.21423 -0.14108 >>>>> SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0 >>>>> LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=47.3 PAK=0 >>>>> LLG=4042 >>>>> SOLU 6DIM ENSE ensemble1 EULER 213.115 0.173 146.741 FRAC >>>>> -0.49931 -0.00269 0.00045 >>>>> SOLU 6DIM ENSE ensemble1 EULER 248.173 0.254 111.665 FRAC >>>>> -0.47091 0.49661 0.00101 >>>>> SOLU 6DIM ENSE ensemble1 EULER 359.399 31.602 180.578 FRAC >>>>> 0.75808 -0.71455 -0.13980 >>>>> SOLU 6DIM ENSE ensemble1 EULER 359.378 31.255 180.361 FRAC >>>>> 0.78370 -0.21555 -0.13830 >>>>> >>>>> >>>>> I remember there is a discussion in CCP4bb about the same >>>>> topic with the focus of pseudo-symmetry or translational >>>>> pseudo-symmetry. Can anybody give some troubleshooting >>>>> about my issue? >>>>> >>>>> Thanks a lot and have a nice weekend, >>>>> >>>>> Jerry McCully >>>>> >>>>> >>>>> >>>>> _________________________________________________________________ >>>>> Windows Live: Keep your friends up to date with what you do online. >>>>> http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009 >>>>> >>>>> >>> Hi Jerry, >>> I am having similar trouble with you. You might want to check out >>> this paper Acta Cryst.(2005) D61:67-74. It is about >>> lattice-tranlation defects and how to correct it. Hopefull it is >>> helpful! >>> Good Luck! >>> >>> Yuan >>> >>> > Hi Eleanor, > Could you explain a little bit more about how to tell the > difference between pseudo-translational symmetry and lattice > translation defects? Thanks a lot! > > Yuan > > Hmm - that is hard.. pseudo translation is relatively harmless - you have 2 or more molecules in the same orientation but in different positions in the unit cell, and the structure factors they generate will have some different properties. For instance the 0k0 in your case will always have k=2n+1 weak because the translation is xt, 0.5,zt ( you can work that out from a SF equation if you like!) And since the xt = 0.02, ie is rather small, and zt = 0, at low resolution all the hkl with k=2n+1 will be weak. use hklview data.mtz and look at h0l then next level , next level etc and you should see this effect.. The only problem it gives in is determining the spacegroup. But phaser will usually sort that out as long as you let it test all SGs . Lattice translation is effectively one form of twinning, you can visualise it as a set of crystals where that lattice are aligned in 2 dimensions but there is slippage along the third. So each "reflection" is in fact the sum of two or more intensities and the twinning analyses should be valid. But as well you have the problem that some classes of reflections are very weak, in the same way as a pseudo translation affects the data. And the twinning tests via moments, H test and Britten test are all distorted by the weak/strong pattern so really the only effective test is the L test, and that too can be badly distorted by anisotropy and other defects. Apparently it is often possible to recognise a lattice defect by looking at the images, if you are good at that. Some classes of reflections will be very streaky ( where there is an overlap between the different crystal fragments) and others sharp. But once the data is integrated that information is lost. Does that help? Eleanor