[phenixbb] R/Rfree discrepancy Phenix vs Refmac
Sabine Schneider
sabine.schneider at mytum.de
Fri Aug 12 06:08:32 PDT 2011
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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