This is very uncommon...
Can you look at the final plot of R and Rfree against resolution.
Sometimes there is an awful hiccup somewhere -
ice rings?
high resolution data somewhat fictional -
low resolution data saturated and also somewhat fictional ..
I also check the completeness which is uin the same loggraph panel.
Eleanor
On 12/09/2011 08:53 AM, Tim Gruene wrote:
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> Dear Petr,
>
> there may be a couple of reasons, e.g.
> - - your data are not really 1.1A, but you simply integrated a lot of noise
> - - you entered some odd command or another option which allows refmac5
> such a deviation
> - - your model is incomplete
> - - surely several more.
> When a well tested program does something unexpected, it is usually the
> user and not the program which misbehaves...
>
> The optimisation of the weighting scheme is based on the geometry of the
> model and not one the gap between R and Rfree.
>
> Cheers, Tim
>
> On 12/08/2011 08:43 PM, Petr Leiman wrote:
>> Dear Tim,
>>
>> I agree with you completely. The question then becomes why does the automatic weighting scheme in refmac allow R and R-free to run away from each other by 8% in a 1.1 A resolution structure?
>>
>> Petr
>>
>> On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote:
>>
>> Dear Christopher,
>>
>> if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be
>> looking at an electron density map with strong model bias, i.e. the map
>> shows the features of the model and not of the data. Although at 1.1A
>> resolution this seems quite unlikely, but that's what might explain this
>> great gap between R and Rfree.
>>
>> Tim
>>
>> On 12/08/2011 06:36 PM, Christopher Browning wrote:
>>>>> Dear All,
>>>>>
>>>>> Question: Has anybody ever refined the same structure using PHENIX and
>>>>> then tried REFMAC to see what happens?
>>>>>
>>>>> I did and I stumbled on something funny. I'm refining a structure at
>>>>> 1.1A resolution which was solved with Iodine phasing using PHENIX
>>>>> AutoSolve. Got a great map and the structure was built almost
>>>>> completely. I had to build a few residues myself, and using the
>>>>> published sequence, I started filling in the residues, but as I came
>>>>> nearer the N-terminus, it looked like the density did not match residues
>>>>> from the sequence. I kept the residues as in the sequence, but as you
>>>>> can see from the PHENIX refined picture (below is the link) it still
>>>>> looks like the amino acid sequence in the crystal does not match the
>>>>> published protein sequence.
>>>>>
>>>>> Out of interest I refined the same file in REFMAC, and now the electron
>>>>> density is correct, and the sequence of the amino acids in the crystal
>>>>> matches the published sequence (see link for picture below). Not only
>>>>> that..... my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC).
>>>>>
>>>>> I've also refined the occupancies of the iodide, however the the output
>>>>> FO-FC map from PHENIX complains and the REFMAC map is fine.....
>>>>>
>>>>> How can this be and what causes this?
>>>>>
>>>>> Link for the pictures:
>>>>> Both maps are at identical Sigma levels in both pictures.
>>>>> PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png
>>>>> REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Chris Browning
>>>>>
>>>>>
>>>>>
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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