[phenixbb] What does mmtbx.twin_map_utils output?

Peter Zwart PHZwart at lbl.gov
Tue Sep 11 12:26:23 PDT 2007


I am refining it myself now, and I think that the problem you describe 
has been solved locally.
The twin map utils unfortunatly doesn't pick jup the free set 
automatically, which probably is the reason why the free R = the R, 
unless you specify the free set in from the command line.

Including twinning in refinement will almost always get your R value to 
something lower than when not including twinning; even if the data is 
not twinned ...

Did you try using a TLS model in the P422 case? Furthermore, is the data 
P422, or is there evidence for the sg to be P4x2y2?


Thanks

Peter






Francis E Reyes wrote:
>
> The model was rebuilt using P422, but I couldn't get the R/Rfree's 
> down from the mid 30s, despite the entire model being built.  Thinking 
> I had a twin problem, I scaled it to C2, the lowest symmetry space 
> group the data collection would allow. I was enthused,however, that 
> twin_map_utils did show a round of refinement where R/Rfree was 30/30 
> at 2.6A, though I/Sig should be > 2 at 2.8 A. I was hopefully trying 
> to get a model to refine using the way twin_map_utils did to produce 
> the low r/rfree until I hit the phenix.refine twinning bug..
>
> FR
>
>
> ---------------------------------------------
> 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
>
>
>
> On Sep 11, 2007, at 12:32 PM, Peter Zwart wrote:
>
>> obs : obs data
>> calc: Fatoms+Fbulk
>>
>> No twinning involved in computation of calc
>>
>> For some reason, the R value between Fcalc for twin related reflections 
>> are all about 14%.
>> I guess you have pseudo symmetry somehow, but I still would not exclude 
>> P422 ...
>>
>>
>>
>>
>>
>>
>>
>> Francis E Reyes wrote:
>>> Specifically I'm asking about the obs_and_calc.mtz file it produces. 
>>>
>>> Thanks
>>>
>>> FR
>>>
>>> ---------------------------------------------
>>> 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
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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