It is interesting and relevant here I think that if you measure
background-subtracted spot intensities you actually are measuring the
AVERAGE electron density. Yes, the arithmetic average of all the unit
cells in the crystal. It does not matter how any of the vibrations are
"correlated", it i
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James
Some comments!
>The diffuse scatter does NOT tell you about the
> deviations from this average; it tells you how the deviations
> are correlated from unit cell to unit cell.
Does this just refer to the scatter near the Bragg peaks? If there is no
correlation from unit cell to unit cell t
Dear Jacob,
Your approach I think it is a sound one for exploring how to gain a
significant potential improvement by harnessing the diffuse diffraction,
which looks rich and varied in many cases ie must surely contain good
structural information. The separation of the various experimental and
cryst
Quoting "Bernhard Rupp" :
I suppose most have read the Acta D editorial already
http://journals.iucr.org/d/issues/2010/01/00/me0408/me0408.pdf
but it seems another creative way of structure generation
has been discovered by some small molecule people:
http://journals.iucr.org/e/issues/2010/01/00
Dear all,
Could I draw your attention to a lectureship recently advertised here in Oxford
at the Laboratory of Molecular Biophysics ? We are looking to appoint a
new faculty member to join a growing body of structural biologists in
a beautiful new building that offers excellent facilities. Applic
Hi Fengxia-
How about increasing the PEG% so you don't have to add as much "other"
cryoprotectant?
Also, have you tried annealing the crystals? I've had success with this when
I've had samples diffract similarly. The simplest way is by blocking the
cryostream for 2-3 seconds (repeat 1-2 times) and
After the success in number of applications, a gentle reminder before the
close deadline (next Sunday)!
=
Practical workshop on the use of longer wavelengths in Structural Biology
*The routine accessibility, on some macromolecular crystallography (MX)
beamlines at SR sources, of photon
Fengxia,
From the images it is clear that the degree of smearing is variable. From
this you can
deduce that you should be able to get sharp images by finding better
cryo-conditions.
There is no magic involved. Your crystallization conditions have little
precipitant
and a lot of water. Hen
Fengxia,
To me the diffraction appears as if the crystals did not freeze well.
So the best option seems to be annealing (as already suggested) or to
try different cryo-protectants.
Did you perform a room-temperature mount? If so, were the spots nice
and round (suggesting the cryo is the cause of t
One other thought following from Kelly's point about room temp check is that
most likely these are thin plates or needles. And I think it was Frank VonD who
pointed out that some of these thin crystals can be physically stressed by the
shape of the frozen cryo formed in the cryoloop. So choose l
Hi,
I am trying to install the latest version and downloaded the .exe file. But
it failed with error message 1911. CCP4Wiki doesn't have any entry for it.
CCP4 6.1.2 (it appears to be 6.1.3)
Windows XP professional system
Here is the error message:
"Error 1911. Could not register type library f
A postdoc position in membrane protein structural biology is available in
the group of Dr Susanna Törnroth-Horsefield, University of Gothenburg,
Sweden. The position is funded for one year and may be extended up two years
depending on the availability of further funding and satisfactory
performance
Did anybody notice the serendipity of the "smeared spots" question just asked
on the bb? I wonder whether, with the proposed new software, this data set
could actually be used to solve a structure? In fact, these images look pretty
similar to those in the NSB paper I cited previously.
Jacob Kel
Dear All CCP4bbers,
Please help me in finding *R-sym I *(observed), *R-merge I*(obseved), *R-Free
Error i*n the data provided below. If I am not wrong, Can anyone suggest me
the difference between R-sym and R-merge?
Thanks in advance for the help.
James*
*
R-values of internal consistency :
==
Hi James,
Both Rsym and Rmerge are agreement factors. Rmerge is used in the case when you
have data from multiple crystals (because you are merging data coming from
these different crystals). Fairly unfrequent nowadays with the high flux beam
lines at SR sources. Otherwise what is quoted is an
I've never been able to discover any difference between Rsym & Rmerge
Phil
On 21 Jan 2010, at 18:34, james09 pruza wrote:
> Dear All CCP4bbers,
>
> Please help me in finding *R-sym I *(observed), *R-merge I*(obseved), *R-Free
> Error i*n the data provided below. If I am not wrong, Can anyone sug
For what it's worth, I've been told that Rmerge was used originally, in
the pre-cryo few images per crystal age, to indicate the R-factor for
merging data collected from multiple crystals. Isym is calculated
identical but refers to data collected from a single crystal.
To be honest I'm not sur
I doubt there ever was a universal convention. When I was young,
Rsym was calculated from the symmetry related reflections on a
single film. With precession photography there could be a lot of
them, but even the oscillation films often had many mates because
the crystal was aligned with a symm
I'm not familiar with this output (XDS?) but I would guess Rw-lin
(not Rw-pim or rim, although those are theoretically more useful)
is the R-factor to use for Rsym (or Rmerge if you are merging datasets
previously reduced from multiple crystals).
I think "observed" means, out of all the spots that
Wow, can I quote this in the response to the next review that I get back
where someone complains about the usage of Rsym? Believe me, I have
seen it twice!
Cheers,
Steve
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Dale Tronrud
Sent: Thursday
Begin forwarded message:
From: Charles Wolfus
Subject: Memorial Service for Warren DeLano
In case you have not already heard, the DeLano family is having a
memorial service for Warren:
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Please join
In addition to the good suggestions already posted, I also suggest:
1. Exploring how your cryoprotection is done in addition to screening
chemical conditions. For example, you may want to test longer
equilibration in cryoprotectant, stepwise increase in cryoprotect.,
very fast swish through cryopr
James Holton wrote:
Looks like you have already gotten several good suggestions,
Many good ones indeed, I tried both csymmatch and origins.com
for the moment.
This mailing list and all its people is extremely helpful.
Thank you very much,
Francois.
> but I also
wrote a jiffy program for doin
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