Re: [ccp4bb] translational NCS & twinning

[lijunliuks]

Donghyuk:

How good were your original images?  If the paeks are sharp and clean, your processing could be easier; or you need more efforts.  The data processing statistics is more important for troubleshooting.

Your showed an apparent SG of p6322, but it does have to be exact, especially when with various NCS.  XTRIAGE output the list of 6(1) related systematic absences but none of them went above 10 I/sig(I),  althought not atypical, have you checked the I's against their neighboring I(0 0 6n) to confirm?  Did you try all possible P6i22 within your phaser search?

With twinning test, the closest low symmetry test would be for P6i and P3i21   and P3i12, the later 2 you seemed to have skipped?  High odered twinning in P3i could be possible but would be hard to deal with.

A C2 lattice could be reindexed to a new one with halved a and halved b, which is possible, but if the new one were still with C2, then it would be cautious.

Lijun Liu

DLX Scientific

发自我的小米手机

在 Donghyuk Shin <sdh...@gmail.com>，2019年1月10日 上午4:22写道：

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?

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



########################################################################

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

---

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1