[phenixbb] multi-xtal averaging vs twinning

[Francis E Reyes]

On a side note, for those who have successfully applied multi-xtal  
averaging,


Under what criteria would one embark on using multi-xtal averaging?

-Same unit cell / s.g. (isomorphism)
-Data was collected from xtals from different conditions?
-MR model shows different/unrecognizable features in 2Fo-Fc maps for  
each xtal individually?
-What if some residues are dynamic (different orientations in each  
xtal) or disordered? Would these show up garbage or not at all in the  
averaged map?

Any *good* (i.e. well detailed) papers discussing the details of multi- 
xtal averaging would be great.


Tom: Are only model phases used? In other words, are/can experimental  
phases used? Would having experimental phases from any of the xtals  
help in cases where the current model is incomplete (say 60%/70% built  
or Rfree in the 30's) ?



On Jun 26, 2009, at 7:39 AM, Tom Terwilliger wrote:

> Hi Frank,
> I have not done this with twinned data....but I would say yes,  
> detwin everything for this step if you can (but of course refine  
> against the twinned data with a twin target).  It is probably good  
> to detwin because the density modification procedure does not know  
> about twinning...
> All the best,
> Tom T
>
> On Jun 26, 2009, at 1:18 AM, Frank von Delft wrote:
>
>> Hi Tom,
>>
>> Yep, that I figured out, but do I need to detwin the native F's  
>> first?
>>
>> Cheers
>> phx
>>
>>
>>
>>
>> Tom Terwilliger wrote:
>>> Hi Frank,
>>> To use phenix.multi_crystal_average you need one more step: take the
>>> model from your SeMet dataset and do MR on it in the native cell  
>>> with
>>> native F.  Now you have the correspondence between the two cells,  
>>> and
>>> you can plug the 2 models and the one phase set and the native F's
>>> straight into phenix.multi_crystal_average to transfer the phase
>>> information to the native (and cross-crystal average).
>>> All the best,
>>> Tom T
>>>
>>> On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:
>>>
>>>> Hi, I'm trying to to figure out how to transfer phases from a  
>>>> twinned
>>>> SeMet dataset to the native one for refinement.
>>>>
>>>>
>>>> 1) SeMet dataset (2.9A) is solved (despite twinning), structure  
>>>> built,
>>>> refines 29/35 (ish)
>>>>
>>>> 2) SeMet crystals are hemihedrally twinned (confirmed by refining  
>>>> with
>>>> twin law), native probably too.
>>>>
>>>> 3) Native dataset (2.7A) has 5A difference in the long cell edge  
>>>> (478 vs
>>>> 483A).
>>>>
>>>>
>>>>
>>>> So I could (and will try to) simply copy the SeMet phases into the
>>>> native dataset, even though CC Fnat and Fsme is rather low  
>>>> (80-20%).
>>>> But would phenix.multi_crystal_average know what to do with  
>>>> this?  It
>>>> has no explicit options, so I expected not.
>>>>
>>>> Or how *would* one approach this?
>>>>
>>>> Cheers
>>>> Frank
>>>>
>>>>
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>>>
>>>
>>> Thomas C. Terwilliger
>>> Mail Stop M888
>>> Los Alamos National Laboratory
>>> Los Alamos, NM 87545
>>>
>>> Tel:  505-667-0072                 email: terwilliger at LANL.gov
>>> <mailto:terwilliger at LANL.gov>
>>> Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
>>> PHENIX web site: http:www.phenix-online.org <http://www.phenix-online.org 
>>> >
>>> ISFI Integrated Center for Structure and Function Innovation
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>>> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
>>> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
>>>
>>>
>>>
>>>
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>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http:// 
> solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web  
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ 
> cbss
>
>
>
>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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