[phenixbb] problem with a twinned data set

Randy J. Read rjr27 at cam.ac.uk
Sun Mar 2 02:03:37 PST 2008


In addition to what has been suggested, another option is to merge the data 
in P1 and look for 8 copies. Now that you have a reasonable refined model 
from the monoclinic solution, this should find a solution. Then you can 
look for the symmetry in the molecular replacement solution to decide what 
symmetry is crystallographic. An easy shortcut is to run a self-rotation 
function on the Fcalcs from the model. (At the moment, I think you'll have 
to go outside Phenix to do that -- we're intending to put a self-rotation 
function into Phaser but it's still on the to-do list!)

Regards

Randy Read

On Mar 2 2008, Pascal EGEA wrote:

>Hi All
>
>This a question of  general Crystallography and use of Phenix to deal  
>with twinned data.
>
>I am having difficulties with a data set. We have data (2.6 ang  
>resolution) that can be scaled and reduced in P222 with a Rmerge of  
>7%, the systematic absences show a screw axis ( it is P22(1)2).
>However MR in Phaser failed in this orthorhombic settings when  
>searching for  2 molecules of the  complex in the AU.
>If we reduce and scale the data in P2(1) and look at the diffraction  
>pattern in HKLVIEW there is  a /mmm symmetry. In the monoclinic P2(1)  
>setting we can find 4 molecules of the complex (by MR in Phaser) and  
>can refine it with Phenix  to a Rfac/Rfree of 28%/34%. 2 molecules  
>have good electron density whereas the two other ones have one of  
>their domain very poorly defined in density. This is looking very  
>suspicious to me and I am wondering if this refined structure is  
>partially wrong?
>
>Meanwhile  I used phenix.triage on the data processed in P222 and I  
>am confused with the output.
>
>##----------------------------------------------------##
>##                   Twinning Analyses                ##
>##----------------------------------------------------##
>
>Using data between 10.00 to 3.36 Angstrom.
>
>Determining possible twin laws.
>
>The following twin laws have been found:
>
>------------------------------------------------------------------------ 
>-------
>| Type | Axis   | R metric (%) | delta (le Page) | delta (Lebedev) |  
>Twin law |
>------------------------------------------------------------------------ 
>-------
>|  PM  | 4-fold | 2.851        | 0.000           | 0.013           | - 
>l,k,h   |
>------------------------------------------------------------------------ 
>-------
>M:  Merohedral twin law
>PM: Pseudomerohedral twin law
>
>   0 merohedral twin operators found
>   1 pseudo-merohedral twin operators found
>In total,   1 twin operator were found
>
>
>---------------------------------------------
>  Analysing possible twin law :  -l,k,h
>---------------------------------------------
>
>Results of the H-test on acentric data:
>
>  (Only 50.0% of the strongest twin pairs were used)
>
>mean |H| : 0.368   (0.50: untwinned; 0.0: 50% twinned)
>mean H^2 : 0.194   (0.33: untwinned; 0.0: 50% twinned)
>Estimation of twin fraction via mean |H|: 0.132
>Estimation of twin fraction via cum. dist. of H: 0.115
>
>Britton analyses
>
>   Extrapolation performed on  0.14 < alpha < 0.495
>   Estimated twin fraction: 0.127
>   Correlation: 0.9955
>
>
>By comparison if I run the detect_twin routine of CNS it tells me  
>that they are no merohedral twin laws for the point group 222 (using  
>the statistical method of Yeates) ? This is  confusing me quite a bit.
>
>
>Assuming that the twinning law suggested by Phenix is correct how  
>should I proceed?
>I have noticed the section concerning refinement using twinned data  
>in Phenix
>phenix.refine data.hkl model.pdb twin_law="-k,-h,-l"  
>detwin.map_types.aniso_correct=true
>
>but It seems I  only have a MR solution in P2(1) but not in P222(1)  
>so how can I refine in P222(1)
>
>I will greatly appreciate your input, many thanks.
>
>
>Pascal F. Egea, PhD
>University of California San Francisco
>Department of Biophysics and Biochemistry
>Robert Stroud Laboratory
>pascal at msg.ucsf.edu
>
>
>
>



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