A postdoctoral position is available in Dr. Fang Li's lab at the Department of
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One correction: Model should after molecular replacement and few cycles of
refinement (perhaps with a little bir relaxed geometry, but not too much).
There is an option to use a model after molecular replacement but it is being
migrated to another program that will have proper tests.
Regards
Ga
Hi Harry,
I laughed when I read your question below "Or is this considered just something
that old folk do?".
At the Australian Synchrotron MX beamlines (MX1 and MX2) we also go old-school
and collect Lanthanum hexaboride powder diffraction data during each user
setup. We collect a single 180
Hi Tim,
There is an option to do unit cell parameter refinement (for all six parameters
in general which can only happen in P1). It is undocumented.
Celrefine/lattice refine all # if you give scale instead of all then only one
parameter is refined.
Cellrefine select . # use only atomic B val
John, I'm sure they were bred by Brother Adam!
There is a nice paper on wax diffraction here:
https://fdocuments.net/document/crystallinity-of-plant-epicuticular-waxes-electron-and-x-ray-diffraction-studies.html
There are others by the DLS team ;-
Also, looks like the d-spacing was 3.72 Angstro
Hi Jessica,
Jens Luebben wrote cellopt for this purpose. It is available from
github, https://github.com/JLuebben/CellOpt
It is based on the idea available in whatcheck, i.e. to optimise the
unit cell parameters based on geometry restraints DFIX/DANG. Those need
to be three-dimensional: I've had
I suppose that this is where the phrase "Mind your own beeswax" comes from 😉
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Edward
> Snell
> Sent: Thursday, July 16, 2020 16:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Quote source inquiry
>
> Not completely re
Hi,
Two aspects:-
Frank Herbstein investigated the precision of unit cell parameters in chemical
crystallography, which I imagine will be of interest:-
https://scripts.iucr.org/cgi-bin/paper?bk0071
Secondly, at the synchrotron, the pure metal foil scan, eg of nickel that I
purchased from Goodfel
That's interesting. I remember the days of wax rings, we even used to do
several at different X-D distances. I sort-of lost faith with the advent of
cryo since I had now idea of how this would affect the wax d-spacing (was it
2.72 Angstroms at rtp?) but ice-rings were always a life-saver to chec
As someone working with continuous rotation electron diffraction, mostly
with small molecules, I am often very concerned about the accuracy of my
cell dimensions. I have to heavily restrain my experimental geometry,
including the detector distance, because they are so unusual compared to
X-ray setu
Not completely related to the question but at one particular European
synchrotron there were a group of beamline scientists that also kept honey
bees. The wax from each hive gave very beautiful powder diffraction patterns
with the scattering being similar but distinctive to each hive. I was fort
Hi Gerard
Indeed. Calibration used to be part of the experiment, but it’s often forgotten
these days (or it’s assumed that someone else has done it to an adequate
standard - fortunately, this assumption is usually valid enough).
Harry
> On 16 Jul 2020, at 12:37, Gerard Bricogne wrote:
>
> D
I think I wasn't totally clear. The structure was refined
with the correct cell dimensions and those fractional
coordinates then were converted to orthogonal as the last
step before sending them to the PDB. Had the depositor
simply sent us the fractional data, we would have changed
them to ortho
There are cases where cell dimensions vary in a very real way. I have a
system in which the unit cell volume can differ by more than 10%. When I
first explored this system in the long ago times, before
cryo-crystallography was a thing, the unit cell dimensions would change
during data collectio
I have a related question. Why calculating/reporting standard deviation for
cell constants is not now mandatory in protein crystallography. Is there
any reason for that (e.g. difficult to calculate or error in calculation).
Now mmcif being the official format and there is mmcif category for esd,
sp
You can change the cell dimensions without spoiling the map fit too much,
but obviously you need to convert deposited orthogonal coordinates back to
fractional using the given SCALEi matrix, than re-orthogonalise with the
modified cell..
Eleanor
On Thu, 16 Jul 2020 at 13:01, Schreuder, Herman /DE
Do you want a high visibility role within a dynamic and innovative biotech
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My guess is that the model no longer superimposed well onto the electron
density map, which should be easy to spot.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Frances C.
Bernstein
Gesendet: Donnerstag, 16. Juli 2020 13:44
An: CCP4BB@JISCMAIL.AC.UK
Bet
Hi Frances,
I'm not surprised. Just correcting (from old orthogonal via fractional to new
orthogonal) will "stretch" bonds ever so slightly. I would have done
rigid-body followed by some all-atom refinement and maybe checked the map and
model fit afterwards (esp. at crystal contacts), and if n
I do not remember the date or the PDB entry but it was during
the time that the PDB at BNL was including distance and angle
outliers in the checking report sent back to the depositor.
It was a not-too-large protein and there were perhaps half a
dozen outliers each on distances and angles which was
Dear Harry,
I think that sharp ice rings (or, better, a powder pattern from silicon
powder) are only part of the solution to the calibration of beam energy, as
there is an interaction with the detector distance. If I recall what I saw
in my now distant days at LURE, a precise energy calibrati
I think most of us are such "excellent" cryo-coolers that for every beamline
shift we have multiple crystals with ice ring diffraction :-)
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Sect
Hi
Does anyone bother collecting a powder image (e.g. Si powder) these days so
they actually have a reference that can be used to check both the wavelength
and the beam centre? Or is this considered just something that old folk do?
Harry
> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt wrote:
No, I only wore Dutch clogs :-) Uppsala was an observer I think so Alwyn and I
could attend the meetings, but we couldn't hire anyone.
--G
On Thu, 16 Jul 2020, Eleanor Dodson wrote:
Well - it was Hamburg high resolution data - I guess we all had a stake in
it.. Good meetings but You were par
There was a case a few years ago (not too many though) where a 1.6 Ã… structure
had been solved using an incorrect value for the wavelength (~5% too low,
leading to a cell that was slightly too small for its contents to be
comfortable). It was later corrected so we could compare their validation
I don't know what the return on investment would be, but after establishing
that there are cell dimension deviations one should actually try to find the
source of the problem. If it is the reported geometry of the experiment than it
is just a matter of changing the cell dimension, but if the wav
Well - it was Hamburg high resolution data - I guess we all had a stake in
it.. Good meetings but You were part of them? Did you wear a Dutch hat?
E
On Thu, 16 Jul 2020 at 12:07, Gerard DVD Kleywegt
wrote:
> Hi Eleanor,
>
> Yes, I remember those meetings, when the UK was still an EU member and
>
Hi Eleanor,
Yes, I remember those meetings, when the UK was still an EU member and Sweden
not yet (so Uppsala couldn't be formally involved) :-)
Did Victor look into this too? I remember Gert doing it. And maybe Tom
Oldfield?
Best wishes,
--Gerard
On Thu, 16 Jul 2020, Eleanor Dodson wro
Hmm - remember Gerard, the EU Validation initiative in the 1990s? We
analysed these effects, or at least Victor Lamsin did, and we applauded him.
Cheers Eleanor
On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein
wrote:
> Hi Robbie,
>
> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
Hi Robbie,
On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
> At the same time if you have a a more relaxed approach to restraints
> than you might find systematic deviations in bond lengths. A test
> for that has been in WHAT_CHECK for decades and it actually works
> surprisingly w
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