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CCP4BB  January 2019

CCP4BB January 2019

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Subject:

Re: translational NCS & twinning

From:

Ethan A Merritt <[log in to unmask]>

Reply-To:

Ethan A Merritt <[log in to unmask]>

Date:

Thu, 10 Jan 2019 10:16:32 -0800

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On Thursday, January 10, 2019 2:11:52 AM PST Donghyuk Shin wrote:
> Dear all,
> 
> I am having tough time with my Xtal data sets those seem to be twinned or have translational NCS, and it will be greatly appreciated if you can give me some advices or comments!
> 
> Data was initially processed with XDS and scaled with aimless without specifying certain space group (SG).
> Aimless picked the P 63 2 2 for the best SG, but the xtriage indicates there is non-origin peak after patterson analysis. (attached log)
> And, I could not get the proper MR-solution from this data sets.
> 
> Because I read that twinning and tNCS cannot be properly distinguished at high SG, I went down to subgroup either P32 or P6 assuming that there is twinning which make data set seems to have apparently high SG. (procedure was same XDS->aimless but I specified the SG to keep them)
> Then, xtriage still indicates there is non-origin peak as before, but found twin laws for the data sets (attached log).
> However, I still could not get the right MR-solution.
> Then, I went even further down to P3 or C2, and xtriage found more twin laws which is make sense because of the lower SG. (attached log)

> Again, I could not get the MR-solution.
> For all the MR running above, I assumed that phaser(ccp4 module) automatically applied tNCS if they present. or should I have to tick on button in the expert parameters?
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Hi Donghuk,

This may indeed be a possible source of problems.   I have recent experience with a
case where aimless/xtriage/phaser all report a large tNCS component, but allowing
phaser to use this information prevents finding a correct MR solution.  I can only
obtain the known correct solution by telling phaser explicitly _not_ to use tNCS.
In my case the true space group is P1 but the angles are all close to 90., causing
most indexing programs to falsely identify it as P2.  I cannot say how or why the
tNCS test triggers, but the known correct solution in P1 does not contain tNCS.

	Ethan


> 
> Then, I went back to the image and processed the datasets with mosflm by checking the indexed spots.
> During this step, I played with the threshold for indexing to follow the strong spot for get correct SG.
> I am not sure whether this is correct or not, but by putting high threshold for indexing (e.g. ~15) I could index the data with C2 which has half dimension for a,b axes (116.348,  67.218, 182.861,  90, 90, 90) to the original unit cell (232.533, 134.202, 182.67, 90, 90, 90).
> With this, I could put 3 molecules in ASU by MR. During refinement, I felt that the R values were not dropping, and I applied twin refinement.
> without twin refinement the R values were (0.39/0.44, work/free), and applying twin refinement gave me significantly better values (0.23/0.26).
> Because there were 6 twin operators which may cause this huge R value drop, I speculate whether this is true or not.
> 
> Your comments will be greatly helpful! 
> 
> With you all the best,
> Donghyuk
> 
> 
> 
> ########################################################################
> 
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-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

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