Dear CCP4 readers
There is currently an opening on the MX beamlines at the Australian
Synchrotron. For the full job information consult the link below.
Regards
Christine
http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron/employment-opportunities/699-science-research-offi
PDE2 full length versus domain only structures, I think.
Artem
On Thu, Jan 12, 2012 at 10:03 AM, Qiang Chen wrote:
> Hi,
>
> I'm working on a multi-domain protein which uses three domains to form
> homodimer, and the full-length structure is available. We have solved the
> structure of one bindi
Hi,
This is a fairly familiar issue. A hydrophobic protein with thiols often
contaminates IMAC columns and this kind of contamination can be difficult
to remove completely. In the past some of the methods that worked included
trypsin or papain treatment, followed by massive amounts of chelating
ag
Katherine,
You are not alone. I have inadvertently destroyed a GE HisTrap column with high
concentrations of proteins that contain many exposed cysteines. In my case the
Co2+ resin turned a very dark purplish-brown and the protein appeared to have
crashed out on the column. I didn't try to stri
Hi all,
I've run into a bit of a protein purification conundrum and wondered if
anyone had encountered a similar situation. I've exercised all of my
google-fu and can't find anything. It's a fairly straightforward setup;
His-tagged protein and Talon Co2+ resin, load lysate, wash with 5 mM
imidazol
Dear Colleagues,
I would like to draw your attention to an upcoming free, educational webinar to
be presented by Max Petersen, Ph. D. titled "Recent Advances in Automated
Protein Drop Imaging." Analyzing vast numbers of protein drops is a time
consuming bottleneck that affects most protein cry
On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine wrote:
>
>> Who needs hydrogens?
>
>
> may be you need to read this (for example):
>
> http://www.phenix-online.org/papers/dz5209_reprint.pdf
>
While this reference is useful, it neglects the role of prior chemical
forces (vdW and electrostatics, fo
This is a forwarded message. For inquires please contact chsfa...@iq.usp.bror
robe...@iq.usp.br
___
The Central Analítica at the Instituto de Química, Universidade de São
Paulo has an opening for a Laboratory Specialist in NMR. The position is
associated with the acquisition of an 800 MHz
Dear all,
I am searching for a tip-truck for Taylor-Wharton LD35 dewars (see figure
below). This tip-truck used to be offered by Jencons but they discontinued the
product.
Does somebody know where you can purchase such a tip-truck?
Thank you for your help,
Kenneth Verstraete
Ghent Universit
Hi,
I am posting this on behalf of our partner group next door. They are really
quite nice and we work together. Contact information is at the end o the
email.
Artem
-- Forwarded message --
We are seeking a talented and self-motivated professional with expertise in
the area of pr
Hi Ed -
There was a peak in the difference maps, as I recall. I believe it
initially got built as a water, but that proved to be too many
electrons, giving a negative peak. I removed the water, but it was
clear that something needed to be there, at which point I started
casting about for al
Matt,
thank you, this is an excellent summary. One question remains - the
lithium peak should be, afaiu, much lower than the water/sodium. Was
there a peak in difference map or was placement based on identifying
something that looked like a coordination site?
Cheers,
Ed.
On Thu, 2012-01-12 at
Pavel and CCP4ers.
I did have my tongue firmly in my cheek when mentioning the hydrogens…
I am well aware of their importance [winking smiley]
T.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Susse
Tony,
Who needs hydrogens?
>
may be you need to read this (for example):
http://www.phenix-online.org/papers/dz5209_reprint.pdf
?
Pavel
Hi,
I'm working on a multi-domain protein which uses three domains to form
homodimer, and the full-length structure is available. We have solved the
structure of one binding domain alone and found its homo-binding mode is
totally different from that of the full-length protein.
Do you know example
>PS: I am grappling with the meaning of resolution in NMR. I can see that it
>could be related to comparable data/parameter ratios, although I am even
>less clear about the weights of NMR restraint weights than in the case of MX...
>some cross-trained person out there who can explain?
Dear Bernhar
3rd Workshop on the Simultaneous Combination of Spectroscopies with
X-ray Absorption, Scattering and Diffraction Techniques - CSX2012
http://www.psi.ch/csx2012
Announcement and Call for Papers
Abstract submission deadline: 1 May 2012
Dear Colleagues,
Please find at the links below the first
On 1/12/12 9:42 AM, Ed Pozharski wrote:
On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote:
Do you have ultra-high resolution? Something I did not…. Are there
many examples in the pdb of proteins with Li+ refined?
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n
On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote:
> Do you have ultra-high resolution? Something I did not…. Are there
> many examples in the pdb of proteins with Li+ refined?
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI
39 in
On 12 January 2012 13:02, Weiergräber, Oliver H.
wrote:
> I think the problem is related to the term "coherence" being used to describe
> both the type of *radiation* and the mode of *scattering*.
> When talking about (xray) radiation, it denotes the phase relationship
> between photons, and the
You can do this with Scala or Aimless. Scale everything first, write out the
scaled unmerged file, then read it again "onlymerge" and a batch selection
(Aimless also gives a cumulative completeness)
Phil
On 12 Jan 2012, at 14:00, Ingo P. Korndoerfer wrote:
> hello,
>
> my poor dementia ridden
hello,
my poor dementia ridden brain has gone on screensaver ...
i need to calculate the completeness and redundancy of reflections in
batches or ranges of batches in a
multi-record .mtz file.
sftools can do this, but the numbers are pretty much meaningless, i.e.,
my feeling is, if i measure
10%
not on my machine (Suse11.3)
Jligand (1.0.25) -> Load Ligand -> type "3GP" -> the ligand looks totally
normal, incl the C6,O6 double bond.
Cheers
Stefan
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Boaz
Shaanan
Gesendet: Donnerstag, 1
In the current version there is a bug and we have fixed it (as far as i know).
It is not JLigand bug, it is libcheck bug.
If you take the version (5.7 version) then it may work better.
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/
You need refmac5.7_linux.tar.gz or refmac5.7_maci
I think the problem is related to the term "coherence" being used to describe
both the type of *radiation* and the mode of *scattering*.
When talking about (xray) radiation, it denotes the phase relationship between
photons, and therefore even a monochromatic beam can be incoherent (whereas a
po
Hi,
You are right. I happen to have 1.0.7 lying around and there 3GP is fine. A bug
must have been introduced somewhere on the way between versions. I wonder
whether it's only 3GP.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of
On 12 January 2012 11:25, Dirk Kostrewa wrote:
> I'm not a physicist - but isn't (in)coherence also used to describe the
> property of sources of electromagnetic waves with constant wavelength? For
> instance, an incoherent sodium vapour light source (only looking at one
> emission band) compared
Dear colleagues,
has anyone of you experienced problems regarding regularization in JLigand?
When I start the first tutorial and load 3'-GMP (3GP), the double bond to the
O6 atom is about twice as long as the remainder of the molecule; the rings are
also highly distorted. Similarly, if I modify
I'm not a physicist - but isn't (in)coherence also used to describe the
property of sources of electromagnetic waves with constant wavelength?
For instance, an incoherent sodium vapour light source (only looking at
one emission band) compared to a coherent Laser, or the incoherent
emission from
On 12 January 2012 10:33, Dirk Kostrewa wrote:
> My understanding of coherence is a constant phase relation between waves.
Correct. For a perfect crystal all the unit cells are identical so
they scatter in phase
and this gives rise to the interference effect we see as Bragg spots,
as you say ari
Dear All,
Can the CCP4 software get mixed with the PHE and ARG?
I use the Coot to build a peptide. 2 fragments of peptides are suitable for one
specific part of electronic density map, and there is only one residue can
distinguish which fragment of peptide is the real peptide fragment for that
> We don't see any change of frequency (or wavelength) in the majority
> of the scattering from disordered regions so it's Rayleigh (coherent)
> scattering. There will be a small amount of Compton (incoherent)
> scattering resulting from the ionisation events which are responsible
> for radiation
My understanding of coherence is a constant phase relation between
waves. Of course, this breaks down for inelastic scattering, but
(in)coherence can also be described without any change in wavelength.
Best regards,
Dirk.
Am 12.01.12 11:27, schrieb Bernhard Rupp (Hofkristallrat a.D.):
Does o
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Bernhard,
without ever having looked at an NMR experiment, intuitively the
resolution of an NMR experiment should be given as the magnitude of the
minimal chemical shift that could be observed/distinguished. Beware that
'resolution' does not nece
On 12 January 2012 09:57, Dirk Kostrewa wrote:
> That doesn't sound wrong to me: the flexible parts are at different relative
> positions in the unit cells and thus their "partial-structure scattering
> waves" do not have a constant phase relation to each other, i.e., they don't
> give a coherent
Does out of phase imply incoherent scattering? I though it means inelastic
Compton scattering?
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk
Kostrewa
Sent: Thursday, January 12, 2012 1:58 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] N
Dear All,
Could someone explain me why i would see density outside both solvent and NCS
masked regions
(which are input essentially the same in this case into DM) --- what i see is
basicly "density" that
is actually just noise - but outside both masks (and which certainly is not
there in non-
Dear Bernhard,
Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.):
Dear All,
I read an interesting statement in an NMR review:
" regions of a protein or
DNA ⁄ RNA molecule that are flexible in the crystal do
not provide coherent X-ray scattering and hence do
not contribute to th
Hi Scott
I may be completely wrong but I worked on a lithium and sodium
inhibited enzyme during my PhD. At the time, it was considered that
your chances of actually seeing density for a Li+ ion were slim to nil.
Only 2 electrons makes them as tough as hydrogens. My efforts went into
trying to
Dear All,
I read an interesting statement in an NMR review:
" regions of a protein or
DNA ⁄ RNA molecule that are flexible in the crystal do
not provide coherent X-ray scattering and hence do
not contribute to the final electron density map. Thus,
for all intents and purposes, they can effectiv
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