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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: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2009-09-02 You may try Andrey Lebedev's Zanuda program from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp If the problem is related due to false origin related with the presence of strong pseudo-translation then this program may be able to sort this out. In some cases it may also correct space group (if the problem is related with overmerging) regards Garib On 2 Sep 2009, at 18:34, Peter Cherepanov wrote: > 1) do you have unexplained peaks in your native Patterson? > (calculate from your model and compare, if in doubt) > 2) do you have both streaky and sharp reflections present on a > subset of your images ? > > if answers to both questions are yes, then you might have a case of > LTD/OD twinning. The latest Acta Cryst D (Sept 2009) has three > papers dealing with such cases. > Looking at packing in your solution you should be able to figure out > the reason for the defect. Test as many crystals as possible: the > defect fraction is not the same in all crystals, so you might get > one with lower defect fraction! > > good luck, > > Peter > > > > On 2 Sep 2009, at 17:48, 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 > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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