Light microscopy and fluorescence techniques permit the analysis not only of
individual proteins but also functional macromolecular complexes, which have
increasingly come into the focus of modern structural biology.
The Advanced Light Microscopy Facility (ALMF) at European Molecular Biology
L
Dear CCP4 Community,
We are trying to find protein or virus crystals that diffract to reasonably
high resolution (2.5 Angstroms or better) and that are very radiation
sensitive at room temperature. "Very radiation sensitive" in this case
means that the diffraction dies after a few frames, for cry
I wonder whether that is why it works as an anti-coagulant? Is it
mimicking nucleic acids? So then would DNA work as an anti-coagulant
as well...?
JPK
On Mon, Apr 11, 2011 at 4:20 PM, Nian Huang wrote:
> Heparin simulates the structure of DNA and RNA, so it has nonspecific
> affinity towards DNA
Heparin simulates the structure of DNA and RNA, so it has nonspecific
affinity towards DNA or RNA binding protein. It has also been used as DNAse
or RNase inhibitor but it is not very good one.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Sat, Apr 9, 2011 at 7:44 PM, Alexandra Deaconescu
w
Hi Edward:
Actually as I mentioned in the original thread, I have 2 proteins, and
wanted to randomly put the smaller one around the larger one, and quickly
tell whether there is some steric clashes. The smaller protein has a
radius about 20A, and therefore I plan to generate a mask around the
larg
Do you really want atomradius 20A?
Molecules separated by 40 A atomcenter to atomcenter will
be in contact, exclude solvent? Maybe you should tell us what you
are trying to do?
Using fft mode atommap to make a protein mask you could use a
low threshold when converting map to mask, which would exp
The next Gordon Research Conference on Diffraction Methods in
Structural Biology will be held at Bates College in Lewiston, Maine,
from July 15-20, 2012.
As in the past, the program will include the latest developments in
methodology covering all aspects of macromolecular crystallography,
from cr
Hi Edward:
Yes, this is really a good way to do it. Now I am trying to generate a
solvent map using CCP4 sfall (MODE ATMMAP). The thing is I want to specify
a large probe radius (~20A), but it seems that sfall can't change the
probe radius at all. Do you know any other tools to do that?
Thanks ag
As suggested, you can probably get good purification of heparin.
If your pet protein has a known specific binding site, you can make it a
personalized column by PCR'ing up arrays of directly repeated binding sites.
The repeats will mis-anneal in subsequent rounds, giving rise to longer and
long
Dear All,
The closing date for applications for Scientific programmers positions at CCP4
is now changed to 26 April 2011. Please refer to the previous job advert at
http://www.ccp4.ac.uk/jobs/msg00396.html and full description of the posts and
how to apply at http://www.ccp4.ac.uk/vacancies.
B
In general, most protein quantification methods
have significant problems with idiosyncracy, because proteins are
quite variable in composition and structure. The best method is to
use is the absorption at 280 nm, but this is quantitatively useful
only if the mol
Hailiang Zhang wrote:
Thanks Edward! Actually Areaimol works well for my problem.
But now I have a new issue looking for some advice. I want to randomly
generate some points in the unit cell and make a quick judgment whether it
is outside of the solvent mask or not. It seems that Areaimol doesn'
We have a Marresearch 300mm Imaging Plate system (equipped with an
interface for a SGI workstation) to give away. The scanner has not been
used since now 5 years. The equipment is located in Talence, France.
If interested, you will have to arrange for the transport. For more
information
On 04/08/2011 05:19 PM, Cale Dakwar wrote:
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so o
On 04/08/2011 12:17 PM, krishan wrote:
Dear CCP4BB members,
We are using a script written in python to generate symmetry mates for a
given pdb file using PYMOL. After generating symmetry mates we want to
combine all the symmetry molecules in a single PDB file with all the chains
having uniqu
That translation is interesting - R3 indexed as hexagonal has a
crystallographic translation of 0.667 0.333 0.333, so this one
indicated by SFCHECK is related.
The twinning is not very severe so it should refine OK from the PHASER
solution.
Is that so?
Eleanor
On 04/08/2011 05:50 AM, ka
Dear Ed,
since you pointed it out I wonder if there is any reasonable (i.e. w.r.t. data
error/ resolution) difference between the interpolated values and the calculated
value. I actually doubt that
Cheers, Tim
On Fri, Apr 08, 2011 at 12:07:21PM -0400, Ed Pozharski wrote:
> Thanks to everyone fo
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