Hi Tom,
very nice tool! It would be good to get numerical values of the plotted
distributions as well, like mean, median, standard deviation and so on.
Best regards,
Dirk.
Am 08.07.10 15:20, schrieb Tom Oldfield:
Sampath
With regard to your question on what sort of statistics you should g
Sampath
With regard to your question on what sort of statistics you should get
within
structure determination you might find this service at the PDBe useful :
http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp
You can view and manipulate distributions of R, Rfree and R-Rfree along
Something else to consider is what is your space group ?
P212121 but truly P21 with twinning fraction close to 0.5 ?
That's one of my recent cases. 1.9 Å data beautifully refined & built but the
Rwork/Rfree gap was 13 percent. After changing the space group and applying the
twin law the gap is 3
"badly built model" reminds me of another possible reason:
if you have an old version of ccp4 installed (before 6.1??), there is a default
weight of 0.3 for refmac between data and restraints.
This value is - in my experience - way too high for "normal" resolution and at
the beginning of refinemen
I do agree with Tim's reasoning in general, but as Pavel also implied
by offering the statistics,
I would not be worried about the difference, but by the unreasonably
high absolute value of Free R for 2.0 A resolution.
I do not think that its simple 'over-fitting' and my worry would not
be
Dear Sampath,
You are right, the gap between R and Rfree is significant and indicates that
your model was overfitted.
Without knowing your data or your model, some reasons for overfitting might be:
- you used automated placement of water molecules (e.g. through arpwaters or in
coot) and never ch
Hi Sampath,
this is how the distribution of Rwork, Rfree and Rfree-Rwork look like
for 'all' PDB structures refined at around 2A resolution. The "<<<"
indicates where your structure stands with respect to this distribution.
Histogram of Rwork for models in PDB at resolution 1.90-2.10 A:
0
Dear all,
I have a question about the R free value. I refined a structure with 2A
resolution. After model building and restraint refinement using Refmac
program, the average B factor was around 50 for all atoms. The R/Rfree were
around 22/34. Then used the TLS refinement choosing entire molecule.
