[phenixbb] R/Rfree discrepancy Phenix vs Refmac

[Sabine Schneider]

Yes, same mtz input file

Sabine

On 08/12/2011 03:04 PM, Antony Oliver wrote:
> Possibly a silly question - but did you use the same R-free reflection 
> subset in both refinements?
>
> Sent from my iPhone
>
> On 12 Aug 2011, at 13:59, "Sabine Schneider" 
> <sabine.schneider at mytum.de <mailto:sabine.schneider at mytum.de>> wrote:
>
>> Hello Partha,
>>
>> At the moment I was more looking, if it makes a difference what comes 
>> out from Refmac, when I feed it different start models; straight from 
>> Phaser, reset B-values, after shaking coordinates, after shaking 
>> coordinates and SA, and so on....
>>
>> I assumed, if I put the output from Phenix (with R/Rfree X/X  
>> reported by phenix) to be identical to the R/Rfree Refmac reports as 
>> START value when it gets directly the output pdb from phenix?
>> I thought the reported R/Rfree values are just something like 'model 
>> vs data'? That's what I am confused about...
>>
>> No twinning, no automated water building, just 1mol/asu, no twinning
>>
>> Sabine
>>
>>
>>
>> On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:
>>> Hi Sabine,
>>> I believe the comparison should be with same input, not output of 
>>> one piped into another.
>>> How different are the geometry? Different programs use different 
>>> algorithm and different xray:geometry term by default. Hence, it 
>>> might only make sense if the RMSD are almost exactly the same. 
>>> Furthermore, is one program detecting NCS  or twining or building 
>>> waters automatically? Then everything is blown up anyway.
>>> In any case, refinemt program A vs. B is an interesting topic! I 
>>> would not start one.. ;)
>>> MFG,
>>> Partha
>>>
>>> On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider 
>>> <sabine.schneider at mytum.de <mailto:sabine.schneider at mytum.de>> wrote:
>>>
>>>     Hello,
>>>
>>>     I am refining a structure at 2.1A solved by MR. For curiosity
>>>     I'm testing things like 'shaking' coordinates, simulated
>>>     annealing, refinement Refmac vs Phenix and so on, to see what
>>>     influence that has on stats, maps etc.
>>>
>>>     For instance after MR I did a bit of shaking the coordinates
>>>     with pdbset (noise 0.1), followed by simulated annealing in Phenix.
>>>     Phenix states after SA:
>>>
>>>     Start R-work = 0.2671, R-free = 0.2992
>>>     Final R-work = 0.2312, R-free = 0.2666
>>>
>>>     When I use the output pdb of phenix directly in Refmac (with
>>>     same mtz as input for Phenix)
>>>     Refmac tells me:
>>>     Initial R factor    0.2392   R free    0.2887
>>>
>>>     So I am quite puzzled about the discrepancy. Or can someone tell
>>>     me if I made an error in reasoning somewhere?
>>>
>>>     Thanks a lot for the help!
>>>     Sabine
>>>
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>>>
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