One postdoctoral position is available immediately at the Center for Membrane
Biology, Department of Biochemistry and Molecular Biology, The University of
Texas Houston Medical School (http://www.uth.tmc.edu/cmb/). The fellow will
focus on structural determination of important membrane proteins
Dear Colleagues,
This is a reminder that the deadline for applications for the 5th annual CCP4
Summer School "From data collection to structure refinement and beyond" is
April 17, 2012. The school will take place from June 19 through June 26, 2012
at the Advanced Photon Source (APS) near Chicag
Dear all,
There is a staff member vacancy for a Research Software Developer at the
EMBL Unit in Hamburg, Germany. The post holder will have a leading role
in technical implementation and scientific development of the ARP/wARP
software for crystallographic structure determination and the buildi
On 2 March 2012 18:01, Jacob Keller wrote:
> Can't there be a "group of atoms?"
For sure, but doesn't a given parameter either apply to a single atom
or to a group of atoms?
Cheers
-- Ian
Can't there be a "group of atoms?"
JPK
On Fri, Mar 2, 2012 at 12:00 PM, Ian Tickle wrote:
> > I'm aware of this document. Personally I prefer "ADP = Atomic
> Displacement
> > Parameters" over anything ele, because, given that Atomic Displacement
> > Parameters can be parameterized in many diffe
> I'm aware of this document. Personally I prefer "ADP = Atomic Displacement
> Parameters" over anything ele, because, given that Atomic Displacement
> Parameters can be parameterized in many different ways, it makes it easier
> to operate with such terms like:
>
> - isotropic Atomic Displacement P
Thanks Ian,
I'm aware of this document. Personally I prefer "ADP = Atomic Displacement
Parameters" over anything ele, because, given that Atomic Displacement
Parameters can be parameterized in many different ways, it makes it easier
to operate with such terms like:
- isotropic Atomic Displacement
> (*) ADP = Atomic Displacement Parameters
But aren't *isotropic* b-factors subsumed under this TLA (three-letter
acronym?)
JPK
On Fri, Mar 2, 2012 at 11:38 AM, Ian Tickle wrote:
> > (*) ADP = Atomic Displacement Parameters
>
> or "anisotropic displacement parameters"?
>
> See http://ww1.iu
> (*) ADP = Atomic Displacement Parameters
or "anisotropic displacement parameters"?
See http://ww1.iucr.org/comm/cnom/adp/finrepone/finrepone.html
Section 1.5 Comments about terminology
Cheers
-- Ian
Hi,
At 3.3A I would recommend trying a TLS model _instead_ of refining
> individual B factors.
may be it is implementation/software/mindset dependent, but in
phenix.refine refining TLS+individual ADP or simply individual ADP(*) is a
better option most of the time at low resolution.
For details
Dear All,
Thanks for all the suggestions. Lot to learn when its low resolution.
I have few more details5th round of refinement gave R/Rfree 0.2016/0.2767
after reducing waters and fixing some outliers and difference has gone up to
7.5%
I have used Buster 2.10.0 for refinement. First round a
I have purified dozens of very high pI viral proteins, and I can't stress
enough the requirement to wash your protein with at least 1M NaCl after binding
it to the histidine collumn. DNA fragments often require a 2M NaCl wash. High
pI proteins are very soluble.
Dr. Paul Kraft
Structural Biolog
Maybe you can this way.
Use Na acetate to elute your protein, then use EDTA to remove the Ni
from your protein, then buffer exchange or dialysis to remove EDTA.
Kevin
On Fri, Mar 2, 2012 at 5:50 AM, Santosh wrote:
> Hi Anita,
> As Artem noted, use of Histrap column at lower pH would not be a
I've found the following article to be useful in defining suitable refinement
strategies at a particular resolution.
1. Mueller, M., Jenni, S. & Ban, N. Strategies for crystallization and
structure determination of very large macromolecular assemblies. Curr Opin
Struct Biol 17, 572–579 (
On 2 Mar 2012, at 16:02, Regina Kettering wrote:
> Rajesh;
>
> I am not sure that you have a high enough data:refinement parameters ratio to
> refine TLS. It just adds more parameters to refine that can lead to
> over-refinement of your model, especially at the 3.3 A.
TLS only adds twenty p
On Friday, 02 March 2012, Regina Kettering wrote:
> Rajesh;
>
> I am not sure that you have a high enough data:refinement parameters ratio to
> refine TLS.
> It just adds more parameters to refine that can lead to over-refinement of
> your model,
> especially at the 3.3 A.
I'm afraid you've
Rajesh;
I am not sure that you have a high enough data:refinement parameters ratio to
refine TLS. It just adds more parameters to refine that can lead to
over-refinement of your model, especially at the 3.3 A.
HTH,
Regina
From: Rajesh kumar
To: CCP4BB@JI
Dear All,
I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type
structure of same protein at 2.3 A. After molecular replacement, first three
rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and 7.35/30.88 %
respectively.In the fourth round I refined with TLS a
Hi Anita,
As Artem noted, use of Histrap column at lower pH would not be a great idea
and unless you want to elute your protein using pH Step gradient
http://www.gelifesciences.com/aptrix/upp00919.nsf/Content/A960DBAAE1C0C945C1257628001D29BB/$file/28404480AA.pdf
You may also consider using CM (Carb
Classical protein purification by IEX, HIC,
GEC, etc. is apparently a dying art. It is typically quite easy to
purify proteins using non-affinity methods from overexpression
mixtures using an AKTA system. (Gosh, in the old days we used to
purify to homogeneity pro
Proteins with high apparent pi value are often tricky because they tend to
bind anionic substances such as nucleic acids, other proteins, glass, etc.
Conversely given that most proteins have acidic-ish apparent pi its often
worth looking into why a particular protein is basic as it may be a fact of
You might be giving too much importance to the THEORETICAL pI of the protein.
If it's supposed to be well charged at pH 7,4 (only a titration curve, and not
simply knowing the pI will tell you this) and it's still precipitating, the
problem might be due to a bad fold, for instance, or to the la
Hi all,
Thanks for the express replies. Your insights along with the article by
Prof. Garib pointed to by Prof. Pavel completes the story for me.
Regards,
ARKO
On Fri, Mar 2, 2012 at 3:09 PM, Steiner, Roberto
wrote:
> On 2 Mar 2012, at 08:01, arka chakraborty wrote:
>
> Hi all,
>
> I will like
On 2 Mar 2012, at 08:01, arka chakraborty wrote:
Hi all,
I will like to know, as a follow up of what Prof. Randy Read said, what should
be done to do the refinement against the measured data and not the detwinned F(
which refmac outputs in the mtz after twin refinement), during subsequent
refi
1) You should use measured data (after scala/aimless/truncate). In general
there may not be one to one relationship between observed data and asymmetric
unit (e.g. non-merohedral twinning) and it would not be possible to bring input
data to output file. Use original data
2) Internally refmac gro
Garib may have more to say, but the first point would be to always include the
original data file as your input MTZ file for any cycle of refinement, whether
you're using Refmac in CCP4 or phenix.refine. (In phenix.refine, if you assign
the R-free data the first time you do refinement, it will
Hi all,
I will like to know, as a follow up of what Prof. Randy Read said, what
should be done to do the refinement against the measured data and not the
detwinned F( which refmac outputs in the mtz after twin refinement), during
subsequent refinements. And also, I would like to know how to ensure
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