[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Chris
Fage
Gesendet: Sonntag, 23. Februar 2014 23:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] High Rwork/Rfree vs. Resolution
Thanks again for the advice, everyone.
As suggested, I tried NCS and TLS in phenix.refine, although my R-factors di
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay
Diederichs
Sent: Sunday, February 23, 2014 2:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] High Rwork/Rfree vs. Resolution
Projects and problems like this are clearly a justification for asking to
deposit not only the results from data
Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage [cdf...@gmail.com]
Sent: Monday, February 24, 2014 12:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] High Rwork
Chris,
On Sun, Feb 23, 2014 at 2:52 PM, Chris Fage wrote:
> As suggested, I tried NCS and TLS in phenix.refine, although my R-factors
> did not budge.
> (...)
> Forgive my ignorance, but I am not sure how to check whether the bulk
> solvent model is reasonable.
>
I figure you used phenix.refin
, February 23, 2014 5:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] High Rwork/Rfree vs. Resolution
Thanks again for the advice, everyone.
As suggested, I tried NCS and TLS in phenix.refine, although my R-factors did
not budge.
I am now giving PDB_REDO and simulating annealing in PHENIX a shot
On Sunday, 23 February 2014 09:16:41 PM Andreas Förster wrote:
> On 22/02/2014 10:15, Mark van Raaij wrote:
> > But I would really want to make a general comment - not ALL structures
> > can be better than the average!
> Except structures from the Lake Wobegon Center for Structural Biology,
> o
On 22/02/2014 10:15, Mark van Raaij wrote:
As the excellent tips that you got indicate, lower R-factors can be
obtained by getting better data (better crystals, better data
collection, better data processing) or better fitting, i.e. refinement.
In this respect, I am impressed by the automatic dat
oops, thanks for correcting me!
Kay
On Sun, 23 Feb 2014 11:28:31 +, Harry Powell
wrote:
>Hi
>
>Kay means, of course, the ACA meeting in Albuquerque, not the IUCr in Montreal!
>
Hi
Kay means, of course, the ACA meeting in Albuquerque, not the IUCr in Montreal!
Authors of the major processing packages will be competing for your attention...
Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge Biomedi
Projects and problems like this are clearly a justification for asking to
deposit not only the results from data processing, but also the raw data
frames. These would allow developers to improve the models underlying their
algorithms, and to find those corner cases where the algorithms break. Th
I agree with the general points that Mark makes. For the basic problem to find
out whether the model quality (and R-values) is limited by the data quality,
you can compare CCwork with CC* - if CCwork is significantly lower than CC*,
then this means that either your model could in principle be im
As the excellent tips that you got indicate, lower R-factors can be obtained by
getting better data (better crystals, better data collection, better data
processing) or better fitting, i.e. refinement. In this respect, I am impressed
by the automatic data processing protocols now being implement
>
> I'm guessing the low completeness of the 1.65 angstrom dataset has to do with
> obstacles the processing software encountered on a sizable wedge of frames
> (there were swaths of in red in HKL2000). I'm not sure why this dataset in
> particular was less complete than the others.
This is b
I can't help but suggest to also try PDB_REDO for tuning refinement.
http://xtal.nki.nl/PDB_REDO/index.jsp
One of the things you get, is exactly what Pavel explains below, how your
structure looks in comparison with others in similar resolution, but also with
the PDB_REDO data bank structures.
Chris,
First, I would try NCS restraints even at ~ 2 A.
Second, any outliers in your diffraction data set that might skew the R values?
Third, have you checked that your refined bulk solvent model is reasonable?
Axel
On Feb 21, 2014, at 6:13 PM, Chris Fage wrote:
> Thanks for the assista
Hi Chris,
I personally would go with your "thick" dataset. 90% completeness is
not stellar, but in my opinion not detrimental, either.
I had one project that persistently yielded crystals that diffracted
to rather high resolution (2.3), but in one direction no lunes were
discernible and - cons
Thanks for the assistance, everyone.
For those who suggested XDS: I forgot to mention that I have tried Mosfim,
which is also better than spot fitting than HKL2000. How does XDS compare
to Mosflm in this regard?
I am not refining the high R-factor structure with NCS options. Also, my
unit cell di
Chris,
what you get is not unheard of but clearly you are not in majority: at
around 1.95A resolution distribution of R-factors in PDB is:
Histogram of Rwork for models in PDB at resolution 1.85-2.05 A:
0.093 - 0.118 : 3
0.118 - 0.143 : 75
0.143 - 0.168 : 821
0.
Dear CCP4BB Users,
I recently collected a number of datasets from plate-shaped crystals
that diffracted to 1.9-2.0 angstroms and yielded very nice electron
density maps. There is no major density unaccounted for by the model;
however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
~0.30,
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