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

Previous message:
Subject: Weird expression behavior
From: Israel Sanchez israelsanfer {- at -} GMAIL {- dot -} COM
Date: 2009-09-02

Next message:
Subject: Re: CNS to PDB format conversion
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

Subject: Re: Rfactor got stuck with a data having alternate strong and weak reflections.
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

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
>
>
>
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CCP4bb navigation

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

Previous message:
Subject: Weird expression behavior
From: Israel Sanchez israelsanfer {- at -} GMAIL {- dot -} COM
Date: 2009-09-02

Next message:
Subject: Re: CNS to PDB format conversion
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02