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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