Hi All,
A user question about the xia2 behaviour has opened a pot of worms, and
I thought I would ask the community for opinions. If (for example) you
are using an automated data processing or analysis tool, and the
systematic absences suggest a spacegroup choice, what would you like to
do:
(1) n
Hi Lu Yongzhi,
It has to be said it is not obvious. However, there are as far as I can
see at least three possible definitions of I/sigma, so here we go:
(1) I/sigma (calculated, corrected perhaps) for individual observations
- sigma based on counting statistics
(2) Mean(I) / Sigma(mean) - that
Dear Graeme,
here is what I would do, or what I would like to have.
If you are able to identify the Laue group of the data with
some degree of certainty, then all of the processing and
scaling should be carried out in this Laue group.
Then, by looking at systematic absences you may give probabil
Dear all,
speaking of I/sigma(I)
when you use scalepack, how do you estimate it ?
nathalie
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Hi Manfred
I agree with everything you say except the last bit about re-indexing!
For those space groups with alternate settings, e.g. those with standard
names C2 or P2221 or P21212, why is it necessary to re-index to the
'standard setting' when the data will have been already indexed
correctly
Dear Ian,
I thought that in cases of for instance P-orthorhombic where
you can have a screw axis along a, b, or c or any combination
of it, the standard is always to make the unique axis the
c-axis. I.e. the longest axis in P222, and P2(1)2(1)2(1), but
the 2(1)-axis in P222(1) or P2(1)22 or P22(1)
LLI agree the difference between sd and SigI are a bit obscure. One
referes to the spread of values about your mean I (The Sd of the
reflection distribution)
SigI is derived from the SIGI values estimated by the integration.
There is some description in the CCP4 study weekend article by Phil Evans
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These decisions are always going to be individual but I have been
pushing for a long time for the mtz output to have a pointgroup at the
data processing/merging stage with a check list of spacegroups in the
order of their probabilities ( as pointless now suggests..) .
There could then be a seper
Hi Manfred
There's a difference between the 'standard' and the 'conventional'
settings of the Bravais lattices and of their corresponding space group
symbols according to ITC Vol A. For most space groups (i.e. all except
those with standard symbols C2, P21212 and P2221 for non-centrosymmetric
spa
I meant to post this response to Pietro's reply to the BB:
I agree that bugs in software are an ever-present source of annoyance,
but the only software in general use that I'm aware of that can't cope
with the conventional ITC-A settings is Arp/Warp (and even this was
definitely true only for the
Dear Colleagues,
We are currently contemplating the acquisition of
an automated imaging system for crystallization screen plates (96-well).
I am aware that Molecular Dimensions sells these
systems ranging in price between 47 and 71 k and
I am inviting your opinions, comments and advice
on th
On Jan 21, 2008, at 14:08, Ian Tickle wrote:
I meant to post this response to Pietro's reply to the BB:
I agree that bugs in software are an ever-present source of annoyance,
but the only software in general use that I'm aware of that can't cope
with the conventional ITC-A settings is Arp/Warp
Hello all,
I have 2 21inch CRTs connected to a stereo capable firegl card and I am
hoping to enable the active stereo on the extended desktop. Stereo works on
a single screen setup but does not on the extended desktop on 2 monitors. I
have a similar setup on an nvidia quadro card using xinerama th
Dear All,
Thanks to Bill Scott, James Stroud and Jürgen Bosch for their responses.
Here is the original email:
We have recently bought a few iMacs for crystallography. I'm not keen on the
supplied "mighty mouse" so I have switched to using a microsoft 3-button wheel
mo
Dear CCP4-programmers,
I have recently installed CCP4 6.0.2 on a Mac G5 running (still)
under OS 10.4. So far it was running OK - until tonight.
When using superposition programmes (TOPP or Superpose) via the CCP4i
I get the following message:
" Information from CCP4Interface script
*
Yes - you are right! It doesnt work on my PC either..
I dont understand the code at all.
Did it work on an older version of CCP4?
Eleanor
Anita Bentley wrote:
Dear CCP4-programmers,
I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under
OS 10.4. So far it was running OK - u
On Mon, Jan 21, 2008 at 06:28:58PM +0100, Anita Bentley wrote:
> I have recently installed CCP4 6.0.2 on a Mac G5 running (still)
> under OS 10.4. So far it was running OK - until tonight.
>
> When using superposition programmes (TOPP or Superpose) via the CCP4i
> I get the following message:
Do you want an imager, or a more sophisticated system that will store plates
and image them according to a schedule?
With imaging, it is important to think about what you want out of the system,
as it is easy to be disappointed with them. The images you get will not be as
good as what you see
Dear Crystallographers,
Does anyone know of a bioinformatics counterpart of ccp4? It seems like
there should really be such an entity, so that folks would not have to write
scripts, reinventing the wheel all of the time. I am trying right now to
manipulate some sequences into various forms, an
On Monday 21 January 2008 15:33, Jacob Keller wrote:
> Dear Crystallographers,
>
> Does anyone know of a bioinformatics counterpart of ccp4? It seems like
> there should really be such an entity, so that folks would not have to write
> scripts, reinventing the wheel all of the time. I am trying
manipulate some sequences into various forms, and I was imagining a "moleman"
homolog for bioinformatics (perhaps seqman?).
as a matter of fact, i did write exactly that program nine years ago -
http://xray.bmc.uu.se/usf/seqman_man.html :-) - not quite a 'ccp4 for
bioinformatics' but indee
Hi,
I have been trying to express a rat protein in bacteria. The MBP-fusion
expressed at very high level (~ 40 mg/L) while the GST-fusion and His-tag only
gave inclusion bodies. The problem is that all protein runs in the void volume
on a size-exclusion column (s-200, hepes, pH 7.4, 200 mM
Hi Chen,
You could try adding some detergent or other solubilising agent (eg
NDSBs) to your buffer.
Have you tried other pHs? If you are sat near to or on the pI of your
protein, it will be at its least soluble and more likely to aggregate.
I've had protein behave like yours at pH 7.5 but behave p
> BioPython
> There is also BioPerl
And BioJava too,
http://biojava.org/wiki/Main_Page
Depend of your computing preference, and the size of your project...
Regards,
--
Watier Yves
PhD Student, European Synchrotron Radiation Facility (ESRF)
Experiments Division / Materials Science Group
ID31 hi
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