Hi James,
using dynamic N-Gaussian approximation to form-factor tables as described
here (pages 27-29):
http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf
and used in Phenix since 2004, avoids both: singularity at B=0 and
inaccurate density values (compared to the raw
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tg@slartibartfast:~/tmp$ phenix.python run.py
0.001 627.413-4.01639e+06 303880
0.1 275.984 275.247 435.678
0.5 92.2049 92.206 93.6615
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Sorry, 6e^-/A^3 (or -6e/A^3 for charge density people) this should
have said.
On 09/20/2012 11:39 AM, Tim Gruene wrote:
tg@slartibartfast:~/tmp$ phenix.python run.py 0.001 627.413
-4.01639e+06 303880 0.1 275.984
Hi All,
I was wondering if anyone has used N-lauryl sarcosine in the lysis buffer
for purifying protein and checked if the protein was functional or
structurally okay
Please let me know
kind regards
--
rashmi
Why don't you calculate the FFT over the whole asymmetric unit? That is the FFT
default I think
Eleanor
But I think the COOT option works too, but it will also require that your input
map covers the asymmetric unit.
Eleanor
On 19 Sep 2012, at 23:25, Niu Tou wrote:
Dear colleagues,
Is
Hi,
We used it in some lysis/refolding buffers.
Sigma marked this biodegradable detergent as Highly toxic by inhalation -
when it's used in toothpastes and shampoos if I am not mistaken. when I
called, Sigma said that since someone published a paper saying that when they
sprayed it into a
Tim, I don't follow your argument: why should the density be 6A^-3 at
the centre of a C atom?
-- Ian
On 20 September 2012 10:39, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
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tg@slartibartfast:~/tmp$ phenix.python run.py
0.001
Thanks Zhijie,
So do you mean to say that your lab regularly uses it in Lysis and
refolding buffers, and the protein/s purified are structurally and
functionally fine and that there is no aggregation caused due to sarkosyl??
kind regards
Rashmi
On Thu, Sep 20, 2012 at 6:23 PM, Zhijie Li
Dear Fred,
You may like to try the CCP4 Package Manager, available from the downloads
page: http://www.ccp4.ac.uk/download/#os=linux
This allows installation of CCP4 components, including Coot, automatically
and will attempt to identify the appropriate version for you (disclaimer: I
have not
Hi Tim,
I'm not sure I understand your argument either. Anyway, I hope this Ralf's
paper (and references therein) will make it more clear:
http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_electron_density.pdf
All the best,
Pavel
On Thu, Sep 20, 2012 at 5:19 AM, Ian Tickle ianj...@gmail.com
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Because C has 6 electrons and without thermal vibrations (T=0/B=0) I
thought you'd catch all six of them with a box of 1A side length.
Is this too simple thinking?
Tim
On 09/20/2012 02:19 PM, Ian Tickle wrote:
Tim, I don't follow your argument:
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P.S.: run.py reads
format_value(%.6g,ug_n.electron_density(0, b_iso))
so I thought the output of the first line states the calculated
electron density a position 0 (0,0,0) for a Carbon atom (top lines) at
the given b_iso values.
Cheers,
Tim
On
Hi Rashmi,
I can't say that we use it regularly. There are only one or two protocols in
our lab that need it in the buffers. I didn't do the actual work so I am not
sure if there was any problem caused by it regarding the protein purification
or functionality. But those protocols are quite
Dear Fred David,
the new CCP4 Package Manager works perfectly on SL 6.3, as does the
wonderful new CCP4 Update program!
The file command for the coot-real executable (version 0.6.2) tells me:
ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked
(uses shared libs), for
Hi all,
Well I did it the hard way, i.e. try all versions until I came across
one version of Coot that runs.
In my hands I did not get a single version to run on SL6.3, 64-bit
version (Dirk Kostrewa had another experience with SL6.3 64 though).
So I installed SL6.3, 32-bit version, and the
Rajan,
This is old news. Ron Kaplan published a lot about sarcosyl extraction of
native mitochondrial carrier proteins from inclusion bodies in the late
1990's, but there is an equally robust literature stating that sarcosyl is a
denaturant. It is very much dependent on a protein's
Hi,
I know this is not quite the place to ask for this but I was wondering if
anybody has/uses a TA Nano ITC machine. We've recently installed one in our lab
and I've been using it a bit now. The problem is that the people who installed
the machine gave us a really small demo and a PDF file of
Does anyone know how to change a two column format .pdf file into plain one
page at a time format.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Dear colleagues,
I would like to draw your attention to an upcoming free, educational webinar to
be presented by Elspeth Garman, Ph. D. titled Radiation Damage in
Macromolecular Crystallography: What is it and why do we care? Radiation
damage inflicted during diffraction data collection in
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