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Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections. |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Rfactor got stuck with a data having alternate strong and weak reflections. From: Yuan Cheng ycheng {- at -} EMAIL {- dot -} UNC {- dot -} EDU Date: 2009-09-02 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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