Hello, it might be to do with the TLS group refinement which is mentioned in
your log file. Maybe try without TLS and see if it makes a difference, to the
B-factors at least.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
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Dear all
The Microscopy & Microanalysis 2021 meeting will be held in Pittsburgh,
Pennsylvania, August 1-5. In addition to 4 days of the world's largest
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On 04/01/2021 14:38, Silvia Napolitano wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The protein is
generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high
B-fac
Dear Silvia,
While high Bs can be a sign that parts of your model are incorrect (and
therefore some careful manual rebuilding may be required), for things like
poorly-ordered surface loops, they can simply be truth.
A point worth remembering for newbies: your goal is to produce the model that
--Individual ADP refinement--
R-FACTORS WEIGHT TARGETS
work free delta data restr
28.36 32.91 4.55 14.984 101.982 0.0795.042
28.25 33.03 4.78 14.788 103.837 0.0795.023
minmax meaniso aniso
Hmm - this is extracted from your log file: it looks more sensible..
2899: b_iso_mean = 66.62
2907: b_iso_min= 63.50 (limit = 1.00)
2908: b_iso_max= 68.13 (limit = 80.00)
2909: b_iso_mean = 66.62
The average B is 66??
I am more familiar with REFMAC and t
Dear Eleanor,
You are absolutely right.
However, in Polygon, you could compare the models selected by resolution, by
size, etc.
I use this occasion to wish you and others a happy New Year !
Sacha Urzhumtsev
- Le 4 Jan 21, à 15:44, Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscma
Dear Silvia,
In addition to your high-B values I would also worry about your high
R/R-free values - I suggest running your dataset through xtriage to
check for twinning (or look carefully at the output of your data
processing - it should also include some checks for twinning).
The B-value
dear silvia,
apart from the resolution, it would be good to know your current refinement
strategy and if you fed the structure to pdbredo yet. How did that turn out?
the polygon values are picked from structures at similar resolution afaik. In
any case, a better list of B-factors is the one you
That polygon is not very useful I dont think. The statistics need to be
given separately for structures solved at given resolutions.
Eleanor
On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson
wrote:
> Well - you dont give the resolution of your data or the "wilson B" which
> will be recorded in the dat
Well - you dont give the resolution of your data or the "wilson B" which
will be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and b)
it certainly should be high..
So more information is needed.
Eleanor
On Mon, 4 Jan 2021 at 14:39, Silvia
Dear Andreas,
the eiger2cbf code also contains a plugin. I have been using it for
at least 2 years with the LIB= keywords in XDS.
The compilation is not automatically switched on with the Makefile, but
it takes very litte adjustment to create the binary plugin-worker and
the plugin plugin.so
It
Dear Graeme, all,
to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to process
EIGER and EIGER2 data collected at the synchrotron, Herbert Bernstein
created a Windows installer for Takanori Nakane's eiger2cbf converter. You
can find it here: https://github.com/nsls-ii-mx/eiger2cbf.
We are seeking highly motivated postdoc to investigate new targets for
treatment of Alzheimer's disease. You will be joining the Structural Biology
Core of an international, NIH-funded consortium (TREAT-AD,
https://treatad.org/emory-sage-sgc/), contributing to testing new therapeutic
hypotheses
Hi All,
Sorry for the slow response - holiday season & all (I am sure many of us needed
a break at the end of 2020)
Windows is currently not super well supported for xia2 / DIALS work and won’t
work at all for xia2 / XDS for the simple reason that XDS is not available for
the platform (hence a
Dear Colleagues
I am looking for a Research Technician in my membrane protein structural
biology group at Imperial College London (South Kensington campus).
Job details are here: https://www.jobs.ac.uk/job/CDG232/research-technician
Happy New Year everyone!
Thomas
--
Prof. Dr. Thomas Meier
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