Dear Gerard,
I was puzzled by the statement that the UCLA anisotropy server characterises
anisotropy in terms of a combination of effects restricted to lie along the
crystallographic axes. That server is built on the anisotropy correction
algorithm in Phaser, and from the beginning Phaser has
As others point out, anisotropy is endemic in protein crystals, and severe
cases make the single number score for Rmerge, CC1/2 etc pretty meaningless
for the outer shell.
But do not throw out the meaningful data at your higher resolution because
of single number stats-
first LOOK at your images t
Dear Khoa Pham,
the question of a formal definition of en "effective" resolution and its
variability with space direction is discussed in
a) Urzhumtseva, L., Klaholz, B.P., Urzhumtsev, A. (2013) " On effective and
optical resolution of diffraction data sets". Acta Cryst., D69 , 1921-1934.
b)
Dear Gerard,
Thank you so much for the very interesting discussions and the recommendation
of using STARANISO. I will submit my data to STARANISO server and keep you
updated.
Sincerely,
Khoa Pham
Dear Khoa,
You are asking a very pertinent question, that will resonate in
(too) many people's minds.
Somehow anisotropy is very much "an inconvenient truth" in MX, as
many things have long been set up and operated on the basis of having
resolution be a single number and of all statisti
Dear Gerard,
Thank you very much for your suggestions.
We actually analyzed anisotropy of the data using UCLA-DOE LAB Diffraction
Anisotropy Server https://services.mbi.ucla.edu/anisoscale/. The question is
that if the data cut in the anisotropically way, should it be deposited to the
pdb.
Si
Dear Khoa,
Thank you for your reply and for the news that your data do show
strong anisotropy.
In such cases, the reflex is indeed to cut the data down to a
resolution where the statistics look more reasonable. However, as
these statistics are computed in spherical shells, i.e. continue
Dear Gerard and James,
Thank you very much for the suggestions. My data was collected at APS.
Yesterday, an expert in my institution kindly inspected my raw data and pointed
out to me that my data are indeed severely anisotropic in the b direction. He
also recommended me to cut the data to 3.2
Dear Khoa,
I would lean in the same direction as James, and say that what
you need is not advice about what refinement program to use, but a
question about whether you could collect better data. With an overall
I/sig(I) of 8.3 and an outer-shell value of 0.5, there is just not
enough oomph in
I am not happy with an Rmerge of 20%. Also what is the Rmerge and
redundancy in the highest shell, i.e. do you really have the resolution of
2.9?
How did you collect this data? SR or lab.
James Phillips
On Wed, Jun 14, 2017 at 8:09 AM, Khoa Pham
wrote:
> Dear CCP4 members,
>
> I am refining
Dear All,
Thank you very much for your suggestions.
I will refine the structure and keep you updated.
Khoa
Hi Khoa,
How many rounds of refine and rebuild have you gone through on the graphics?
Have you tried Lorestr in CCP4 (Automated refinement of macromolecular
structures at low resolution using prior information, Oleg Kovalevskiy, Robert
A. Nicholls and Garib N. Murshudov).
Ben
[At 2.9A res
The R factors may be high because the structure is imperfect - almost
inevitable at that resolution - but also there are often serious
difficulties with scaling at this resolution . If you are using REFMAC look
at the v wrt resolution plot at the end of refinement (follows R
and Rfree plot v reso
If you dont use Phenix, print the figures of
https://doi.org/10.1016/S0969-2126(02)00743-8
and use them beside your screen. Helps a lot if you wanna have a quick look at
Rfact distributions..
>>> Paul Emsley 14.06.17 15.25 Uhr >>>
On 14/06/2017 14:09, Khoa Pham wrote:
> Dear CCP4 members,
>
On 14/06/2017 14:09, Khoa Pham wrote:
Dear CCP4 members,
I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are are
0.34/0.37, respectively.
My question is that these Rwork/Rfree are acceptable for publication.
If you have Phenix, try POLYGON. That will give you a goo
Dear CCP4 members,
I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are
are 0.34/0.37, respectively.
My question is that these Rwork/Rfree are acceptable for publication. If not,
how can I reduce them?
Thank you.
Khoa
The table of statics.
Space group
C121
Resolu
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