[phenixbb] multi-xtal averaging vs twinning
Tom Terwilliger
terwilliger at lanl.gov
Fri Jun 26 08:08:55 PDT 2009
Hi Francis,
I think multi-crystal averaging is going to be useful only if the
crystals are completely different or the amplitudes are nearly
uncorrelated. In cases where there are only small changes the
averaging procedure has almost nothing different in the two structures
to work with and it won't do much. Another way to say this is that
multi-crystal averaging works because two or more very different ways
of sampling the Fourier transform of the molecule are occurring, and
each must be consistent with the corresponding measured data. If the
molecules are nearly the same and the measured data are nearly the
same in all cases, then there are few constraints on the phases.
Yes, experimental phases can be included in multi-crystal averaging,
just as for NCS averaging. And yes, experimental phases are most
helpful.
If some regions are different in the different crystals, then the
masking procedure needs to be adjusted to exclude the variable regions
from the averaging process.
Perhaps someone else can suggest a good paper to read on this. Kevin
Cowtan's paper on dmmulti is listed on his program documentation as:
K. Cowtan (1998) Joint CCP4 and ESF-ECBM Newsletter on Protein
Crystallography, 31, p34-38.
All the best,
Tom T
On Jun 26, 2009, at 8:37 AM, Francis E Reyes wrote:
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>> 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
>>>> 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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>>
>>
>> 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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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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