[phenixbb] multi-xtal averaging vs twinning
Francis E Reyes
Francis.Reyes at Colorado.EDU
Fri Jun 26 07:37:56 PDT 2009
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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>> _______________________________________________
>> phenixbb mailing list
>> 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
> 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
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090626/311049bd/attachment-0003.htm>
More information about the phenixbb
mailing list