Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: rudenko {- at -} UMICH {- dot -} EDU rudenko {- at -} UMICH {- dot -} EDU
Date: 2009-09-02

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Subject: 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:
> 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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: post-doctoral fellowship in Ann Arbor, Michigan
From: rudenko {- at -} UMICH {- dot -} EDU rudenko {- at -} UMICH {- dot -} EDU
Date: 2009-09-02