Dear Ivan,
well, with diffraction anisotropy you don't really have a choice, and it
would be too bad to not include all those good higher resolution
reflections.
Diffraction anisotropy follows an ellipsoid, and staraniso gives you the
ellipsoid completeness, which I think is a very useful nu
Temperature is a very interesting variable. I observed opposite solubility
effects in the same protein as a function of buffer and I believe the
crystallization center at my institute (http://getacrystal.com) has seen a
rapid uptake in lower temperature crystallization such that a dedicated ima
Dear CCP4BB,
There seems to be a general consensus for extending data to higher
resolution to include as much meaningful data as possible. "Meaningful"
can be defined in different ways. I heard/read opinions such as 0.5
CC1/2, 0.3 CC1/2, 0.15 CC1/2, and stepped (paired) refinement. The
latter
Interesting topic,
Certainly the two papers suggested by Georg are relevant, and I fully agree
with the comments from Daniel that it is hard to predict the behaviour of any
given protein from a statistical analysis of proteins in general.
I find it interesting that even with the use of incubato
Sergei,
That depends heavily on the protein, so I don't know if a statistical study
will accurately reflect the
importance of temperature. With some proteins, no matter how thoroughly
you sample chemical
space, temperature is critical, and a study would have to focus on such a
protein. The data
Hi Sergei, this publication should be useful for you.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756611/
Additionally it is proposed that when your protein is not so stable
(lower Tm), one should incubate the screens at 4C.
http://scripts.iucr.org/cgi-bin/paper?S0907444911036225
Br, Georg
Dear Colleagues,
The details, including all abstracts, for the IUCr Satellite at ECM32 Vienna on
Data Science Skills in Publishing for Editors, Authors and Referees can be
found here:-
https://forums.iucr.org/viewtopic.php?f=39&t=419
Best wishes,
John
Emeritus Professor John R Helliwell DSc
Ch
Ernst,
Depositing images is very easy these days with services like SbGrid,
proteindiffraction.org (also known as IRRMC), and Zenodo.
For example, for depositing images to proteindiffraction.org (which is
run by Wladek Minor) you just need to create an account, tar your
images, upload them t
Clemens,
I have not looked at the structure, but the issues you described are
alarming. It is a little sad because the paper itself seems very
comprehensive and rigorous.
It is great to hear so many voices advocating for depositing raw images.
I hope more researchers will be convinced to do
Hi Clemens,
thank you for looking into this! To me, a "structure" that has a few sequence
shifts does not appear useful at all - rather, it taints the PDB. This one
should be blacklisted, like 6MO[0,1,2]. It's painful to learn that despite all
the validation that is performed before and at depo
Hi Sergei
We did some data-mining on this way, way back, in 2004.
See the second section in this link
https://www.douglas.co.uk/PDB_data.htm
When you consider the *non-standard *temps - ie NOT 4C or 20C - it *looks*
as though the higher-end temps *may *work better. But of course it's hard
to
Dear all,
I would like to thank all the comments, specially from Kay and Andy.
The space group was correct P212121. More than 100 sites were found with
occupancy higher 0.5. The keywords mentioned by Andy and the improvement of the
data consistency at low resolution as pointed by kay seemed to
Dear all,
I wondered if someone could point me to a recent study on the importance of
temperature during initial search for crystallization conditions. It would be
interesting to see any real statistics on this subject.
We typically try to perform screening at at two temperatures, such as
du
Hi Ivan,
On Wed, Jul 31, 2019 at 05:32:24PM -0400, Ivan Shabalin wrote:
> And Rfree of 36% seems really high.
If you look at the maps (e.g. after some re-refinement with your
favourite refinement package) it seems as if there are a few sequence
shifts (around and after A78), some poor density and
Dear CCP4BB,
The wwPDB are pleased to announce the availability of PDB versioning,
allowing depositors to update their entries while retaining the same PDB
accession code.
Depositors can now submit new coordinates for existing entries.
Initially, this is limited to PDB entries that were subm
Dear Ernst,
There are several ways to deposit raw data, such as IRRMC, SBGrid and
Zenodo. The data are findable through a doi. During the depostion in the
PDB the doi linking to the raw data can be provided. See e.g.
http://www.ebi.ac.uk/pdbe/entry/pdb/5cy2 where is link to the raw data
in S
Dear All,
A postdoc in structural bioinformatics/ in silico drug design/machine
learning applied to GPCRs is available at the Centre of Membrane Proteins
and Receptors (COMPARE), a vibrant joined venture between the Universities
of Birmingham and Nottingham. This is a collaboration between the grou
Dear Ernst,
depositing raw data would add about 100 Bytes of storage per structure to the
RCSB, about the length of a DOI. This is because there are existing
repositories for data storage: data.sbgrid.org (only data related to an
already published manuscript), zenodo.org, and a few more.
They
I totally agree with the deposition of raw data along with the coordinate
set(s). It is the only way to independently validate a model that has been
generated by somewhat subjective procedures of data reduction and scaling,
structure solution and refinement.
More importantly, algorithms and pr
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