Dear All,
Applications are invited for a PhD studentship at the Manchester
Institute of Biotechnology, University of Manchester.
The project will involve the structural and functional characterization
of food allergens and their complexes. The techniques used will include
cloning, protei
Would the CCP4 program BLEND be a suitable initial option? And then the
anisotropic server?
Tony.
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On 12 Nov 2014, at 21:29, Robert Keenan
mailto:bkee...@uchicago.edu>> wrote:
I have three datasets of varying quality collected from different regions of a
Hi Wolfram,
it took me a while until I realized that you mean "overfitting" when you said
"o-word".
You can abuse XDS in a number of ways, and I would call them "overfitting the
data" although that would be using the word in a somewhat strained way:
reducing WFAC1 below 1, decreasing REFLECTIO
Hi Bob,
we have done elliptic truncation before merging/scaling as lined out in
2012 Zebisch (JMB).
However, I see no reason not to scale the 3 runs together with aimless
(to lets say 3.4A) and then subject the resulting merged file
to the sawata server.
Best,
Matthias
-
I have three datasets of varying quality collected from different regions of a
single crystal. In each case, the data are anisotropic (from Aimless using
CC1/2>0.5):
Dataset 1: 3.5, 3.5 5.5 A
Dataset 2: 4.2, 4.3, 4.8 A
Dataset 3: 3.7, 3.9, 4.4 A
I initially took a simple-minded approach an
Hello Kay,
you said the o-word, and you are familiar with the inner workings of XDS.
Has the data-to-parameter ratio in even complex scaling models become so
small that a doubling (worst case) of model parameters would be a serious
concern? Could one detect such overfitting by, say, comparing (mole
Hi,
Our experience was the opposite. Ours did not work well and completely
broke soon after. This incubator quickly turned into the largest door
stop in the lab. I'm sure ours was just a lemon, but I thought I'd still
mention it to warn others.
I am still interested in hearing what models of
This is a test
Sent from my Windows Phone
Hi Kay,
thank you for the clarification. I had understood that using XSCALE
after CORRECT does no harm, but did not understand that the reason lies
in the consistent choice of support points rather than not repeating
what might already having been done.
Regards,
Tim
On 11/12/2014 04:32 PM, Kay
On Wed, 12 Nov 2014 15:32:04 +, Kay Diederichs
wrote:
...
>It then, in a second step, re-determines all scale factors (exactly as CORRECT
>does for the individual data sets), at the exact same supporting points that
>CORRECT used. (This avoids over-fitting which would result from a scaling
Hi Tim,
this is incorrect.
XSCALE determines the relative scale and B in a first step (this is what you
describe).
It then, in a second step, re-determines all scale factors (exactly as CORRECT
does for the individual data sets), at the exact same supporting points that
CORRECT used. (This a
*2014 BCA-BSG Winter Meeting*
*The 2014 BCA-BSG Winter Meeting will take place on the European Photon
and Neutron (EPN) Campus (hosting the European Synchrotron Radiation
Facility and the Institute Laue Langevin), Grenoble, France on 15-17
**December 2014. *The meeting will be themed around op
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Dear Jeorge,
the 'ghost' could be explained by a shift of an entire section, i.e.
you have to split several residues into A+B, not only the MET.
The cylR2 structure in 2XJ3 is one example where this was necessary.
Best,
Tim
On 11/12/2014 11:23 AM,
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Dear Anuar,
this depends on the crystal you are planning to measure. Will they be
small so that you need to go for high intensity, or will they be large
so that you can go for high quality (flat profile beam). Your budget
will also be a limiting facto
That looks really odd - the whole MET has a negative/positive ghost
Second conformations usually branch at the CB, and dont look like that.
Are you sure you havent somehow got two MET residues in the coordinate set
? Turn on cysmmetry display in coot and look for clashes around there.
Does the
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Dear Wolfram Tempel,
there might be some confusion about terms.
It is correct that xscale scales several data sets together. However,
in crystallography, 'merging' might be the better term for this process.
Crystallographic 'Scaling' is far more com
Dr Claudia Alen Amaro
Scientific Project Manager
Instruct: An Integrated Structural Biology Infrastructure for Europe,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Headington OX3 7BN, UK
Tel: +44 1865 287808
email: clau...@strubi.ox.ac.uk
Follow us on twitter @i
Hi everyone,
My institute is decided to purchase an in-house X-ray diffractometer.
Unfortunately i do not know what is the basic requirement that we should look
for before we can select the equipment. I hope to get some guideline that will
be useful for me to make a better decision on which XRD
Hi Jeorge,
The simplest answer is that you have multiple positions for the Methionine. So
you can try adding in an alternate position for it. However, you didn’t mention
the sigma cutoff or e-/A^3 for either of your density maps. Its quite possible
that your fofc map is just scaled way down and
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