> On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote:
> > > Response to off-board mail:
> > >
> > > >How about [calling them] non-centro-symmetric space groups, as I
> often tell my students?
> > >
> > > Almost, but not exact enough.
> > >
> > > The 65 are only a subset of non-centrosymmet
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Dear Mirek,
can you check shelx c/d/e are actually in your path when you start
ccp4i? You can open a terminal and type 'shelxc' to check and then
start ccp4i from the very same terminal - are shelx c/d/e still greyed
out?
Best,
Tim
On 04/30/2014 01:
Dear All
I am facing problem in installation of ShelxCDE on CCP4 6.4.0. I have
installed CCP4 and all the programs are running successfully. I copied and
pasted ShelxCDE executables into CCP4 bin. Earlier also I adopted the same
procedure to activate ShelxCDE on CCp4 interface and it worked. But
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Dear Shanti Pal,
when you download the shelx binaries the executable flag is not
necessarily set. Can you check with 'ls -l $CBIN/shelxc' if this is
the case? You can set it with 'chmod +x $CBIN/shelxc'.
Best,
Tim
On 04/30/2014 11:51 AM, Shanti Pal
Hi all,
Has anyone experienced catalytic metal ions disappearing during data collection
?
If so, is there a way of preventing it?
D.
Dean Derbyshire
Senior Research Scientist
[cid:image001.jpg@01CF6470.5FA976D0]
Box 1086
SE-141 22 Huddinge
SWEDEN
Visit: Lunastigen 7
Direct: +
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Dear Dean,
this is probably a very common observation: X-rays produce reducing
electrons and as you reduce a metal I imagine it does not like its
chemical environment as much as it did highly charged.
Everything you can do to avoid radiation damage s
Dear all
I am working on a metalloprotein which probably contains Ca at its active
site..The sulfur containing amino acid constitutes almost 5.4% of the total
amino acid residues of this protein..I have collected the data at home
source (CuKalpha=1.54A)..Since f'' of Sulfur is 0.56 and that of Ca
Can the radiation damage gurus comment on this ? I know there is a problem with
radiation damage changing the valence state of metals, but I don't remember
hearing about the metal actually being lost due to radiation damage. Is this
really common ?
Thanks,
Andrew
On 30 Apr 2014, at 11:46, Tim
Dear Faisal,
you could use Phenix to do an f’’ refinement against the data like described
here:
Liu, Q., Liu, Q. & Hendrickson, W. A. (2013). Acta Cryst. D69, 1314-1332.
best regards,
Tobias
On 30 Apr 2014, at 14:01, Faisal Tarique wrote:
> Dear all
>
> I am working on a metalloprotein w
Attenuate the beam and take many more frames such that you get a full dataset,
albeit at slightly lower resolution, before the metals go away. In other words,
reduce dose/degPhi.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dean
Derbyshire
Sent: Wednesday, April 30
Dear Pilatus/Radiation Damage Cognoscenti,
I read a few years ago, before the advent of Pilatus detectors, that the best
strategy was a sort of compromise between number of images and detector readout
noise "overhead." I have heard that Pilatus detectors, however, have
essentially no readout no
Dear Dean (and Andrew),
I am certainly no radiation damage guru, but at the RD8 Workshop in
Hamburg 3 weeks ago (http://www.rd-eight.org/RD8-01/) I heard a talk by
Pernille Harris about the photoreduction by X-rays of Cu(II) to Cu(I) in a
Cu-insulin crystal.
Tim's description couldn't b
Hi Jacob,
I'll take a first crack as I am sure many will follow.
It is true that with CCD detectors one has to be careful how small an
oscillation range to use for a frame before read noise starts to eat into the
data quality.
Pilatus offers two major new features - is fast and is photon counti
My comments:
Such observation is very uncommon for metals involved in catalysis by
proteins. I have seen quite a few such structures involving Mg, Ca, Fe,
Mn, Zn and most of the radiation damage was not at the catalytic metal. In
case of Fe once I noticed slight shift in the position of the Fe ion
Well - this is pretty common, and really doesnt matter.
I just let SHELXC/D give an "occupancy" to its anom scatterer solutions
and assume that the stronger one is Ca. But in fact it wont matter at all
for the phasing, and IF the experiment works it is easy to sort out S from
Ca in the final map.
Dear Dean,
You have already received excellent insight into radiation effects on metals.
From personal experience, it doesn't take long for the metal occupancy to go
down to 80%. Of course it is not anywhere near "disappearing" but then again,
we don't know the details of your data collection a
The anomalous signal will always come from both Ca and S and any other atoms in
the crystal. One can determine whether an anomalous difference Fourier peak is
from a sulfur on a cysteine, methionine from the model, right? As for whether
a peak that is not part of an amino acid id Ca++ or Sulfu
If metal ion will be sensitive to radiation depends on its redox chemistry
and not its X-ray properties. For a metal to be affected by radiation dose
it needs to be reduced by free radicals. However, such metals are rarely
(by gene counts or deposits in PDB) present in catalytic sites of enzymes.
T
Hi
Marcus Mueller (from Dectris, who develop and manufacture the
Pilatus) did some work on this a couple of years ago and determined
that an oscillation angle ~ 0.5x the mosaicity of the crystal (using
the XDS value of mosaicity, which is not the same as Mosflm's); the
abstract says -
T
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Northwest Crystallography Workshop
http://oregonstate.edu/conferences/event/nwcw2014/
June 20-22, 2014
The (Pacific) Northwest Crystallography Workshop is a regional
gathering of people who are interested
@ Jim
Me neither, i should read before i reply, my fault.
Tobias
On 30 Apr 2014, at 17:15, Jim Pflugrath wrote:
> The anomalous signal will always come from both Ca and S and any other atoms
> in the crystal. One can determine whether an anomalous difference Fourier
> peak is from a sulfu
I myself have never seen a separate peak that was a single sulfur atom.
I've seen, in a moderately-radiation-damaged dataset, little shards of
anomalous scattering density in Phaser-generated LLG maps. They were in the
interior of the protein, and the closest possible atoms were sulfurs. They w
Dear Dean
An example, albeit not a metal, can be found here:-
http://journals.iucr.org/s/issues/2007/01/00/xh5011/xh5011.pdf
Such specific damage has a long history:-
http://www.sciencedirect.com/science/article/pii/0022024888903223
An X-ray sensitive metals centre is the Mn5Ca OEC of PS II and d
>The question about metal sensitivity to radiation cannot be answered in
>general; it needs to be discussed in specific chemical coordination
>context.
Agreed. The author of the original question should have provided more details
about the metal in question, about the samples and the way experime
Are these metals there in the beginning to experiment before radiation damage
“destroy” them? Easy to check if X-ray fluorescence facility is installed on
the beam line you are measuring.
It is sensitive technique and we constantly use it in the beginning of every
measurement.
FF
Dr Felix Frol
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