Re: [phenixbb] Possible Twinned data

Yuri, I would refine in parallel with and without the twin law and check the resulting maps and R-factors. I had a case where the twin fraction was 0.06, which I expected to be negotiable. When I included the twin law in refinement, my R-factors dropped dramatically. It's usually the best rule of thumb that you have the right space group / molecular replacement solution / twinning / etc. Good luck, Kelly ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 ******************************************************* On Thu, Jun 9, 2011 at 3:38 PM, Yuri wrote:

Hello phenixers, I am a little bit at loss since this is the first time I have encountered this situation. I just collected preliminary data on a ligand soaked crystal. It goes to about 1.85 A. The centrics and acentrics reflections tests look a little deviant from ideal untwinned. I was looking at my xtriage log file and it seemed to me like I have some twinned fraction. Phenix says not. I realize too my completeness is not good. Any educated insight would be helpful as I have never dealt with twinning (if this actually the case). Log file section: Wilson ratio and moments

Acentric reflections /<I>^2 :1.650 (untwinned: 2.000; perfect twin 1.500) <F>^2/ :0.839 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.649 (untwinned: 0.736; perfect twin 0.541)

Centric reflections /<I>^2 :2.099 (untwinned: 3.000; perfect twin 2.000) <F>^2/ :0.749 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.703 (untwinned: 0.968; perfect twin 0.736)

NZ test (0<=z<1) to detect twinning and possible translational NCS

----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.052 | 0.095 | 0.171 | 0.248 | | 0.2 | 0.126 | 0.181 | 0.285 | 0.345 | | 0.3 | 0.197 | 0.259 | 0.371 | 0.419 | | 0.4 | 0.271 | 0.330 | 0.440 | 0.474 | | 0.5 | 0.334 | 0.394 | 0.499 | 0.520 | | 0.6 | 0.394 | 0.451 | 0.553 | 0.561 | | 0.7 | 0.447 | 0.503 | 0.600 | 0.597 | | 0.8 | 0.497 | 0.551 | 0.629 | 0.629 | | 0.9 | 0.541 | 0.593 | 0.660 | 0.657 | | 1.0 | 0.581 | 0.632 | 0.697 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.062 | | Maximum deviation centric : 0.078 | | | | _acentric : -0.050 | | _centric : -0.021 | -----------------------------------------------

L test for acentric data

using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8

Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.270 (untwinned: 0.333; perfect twin: 0.200)

The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available.

Cheers, -- Yuri Pompeu _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb