On 03/12/2014 09:02 PM, Keller, Jacob wrote:
The Fourier transform of electron density is a complex scattering amplitude
that by the axiom of quantum mechanics is not a measurable quantity. What is
measurable is the module squared of it. In crystallography, it is called either
F^2 (formally eq
>The Fourier transform of electron density is a complex scattering amplitude
>that by the axiom of quantum mechanics is not a measurable quantity. What is
>measurable is the module squared of it. In crystallography, it is called either
F^2 (formally equal F*Fbar) or somewhat informally diffractio
On 03/12/2014 04:15 PM, Keller, Jacob wrote:
For any sample, crystalline or not, a generally valid description of
diffraction intensity is it being a Fourier transform of electron density
autocorrelation function.
I thought for non-crystalline samples diffraction intensity is simply the
Four
Posted on behalf of Peter Zwart in the Berkeley Center for Structural
Biology:
Dear All,
The Berkeley Center for Structural Biology at Lawrence Berkeley National
Lab is looking for a postdoctoral fellow to work on the development of
computational methods aimed at improving the overall quality of
Hi,
> Is there a way to tell REFMAC that there are covalent bonds across asymmetric
> units?
Try this (example from 3gbi.pdb) for DNA:
LINK PDC B 119 O3' DA B 125 1555 2555 1.61
LINK O3' DA B 125 PDC B 119 1555 3555 1.61
>For any sample, crystalline or not, a generally valid description of
>diffraction intensity is it being a Fourier transform of electron density
>autocorrelation function.
I thought for non-crystalline samples diffraction intensity is simply the
Fourier transform of the electron density, not it
I haven’t tried this in a long time, but in the old days, we would have simply
refined one strand.
On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov wrote:
> Colleagues,
>
> We have determined a structure of a palindromic DNA molecule, in which one
> half of the DNA is in the asymmetric unit. Is the
Colleagues,
We have determined a structure of a palindromic DNA molecule, in which one
half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC
that there are covalent bonds across asymmetric units? Without such "LINK"
records in the PDB file, REFMAC treats this as a non-covalent i
AFAIK, Dr Smart now works at Global phasing.
https://www.globalphasing.com/people/osmart/
HTH,
Dave
Dr David C Briggs PhD
http://about.me/david_briggs
On 12 Mar 2014 19:46, "Appu kumar" wrote:
> Hello everyone,
> I request all of you to please help in getting
> the
Hello everyone,
I request all of you to please help in getting
the source of hole programme which is required to visualize the cavity
running through the channel in protein structures. This programme is
written by Dr. Oliver Smart. Despite of exhaustive search on various
Dear Jacob
For a review of this topic see
http://www.tandfonline.com/doi/full/10.1080/08893110310001643551#.UyCVLikgGc0
I also refer you to the more recent OUP IUCr book Chayen, Helliwell and Snell
ie which includes these topics:-
http://global.oup.com/academic/product/macromolecular-crystalli
How to approach the analysis of such a problem:
For any sample, crystalline or not, a generally valid description of
diffraction intensity is it being a Fourier transform of electron density
autocorrelation function. There are obvious normalizations involved. For
crystals, this autocorrelation fun
Not sure I understand why having statistical disorder makes for streaks--does
the crystal then have a whole range of unit cell constants, with the spot at
the most prevalent value, and the streaks are the "tails" of the distribution?
If so, doesn't having the streak imply a really wide range of
Dear Stephen,
I have seen a similar effect in the structure of
F1-ATPase complexed with the full length inhibitor protein. The inhibitor is a
dimer, and it actually couples 2 copies of the ATPase, but it crystallised with
only one copy of the ATPase per asymmetric unit.
On 03/12/14 11:52, Kay Diederichs wrote:
...
Account creation now uses a "Captcha" which is not of the boring type,
but rather challenges your expertise in telling cats from dogs.
I have heard that this algorithm can be fooled by cosmetic surgery.
http://www.condenaststore.com/-sp/No-Caption
Zbyszek - do you have any measure of unintegrated streaks?
It could be a help to at least have a rough score.
Eleanor
On 11 March 2014 20:04, Zbyszek Otwinowski wrote:
> Shape of the diffraction spots changes in the statistical disorder <-->
> > twinning continuum. At both ends spots shape is l
Dear all,
today we re-opened account creation for CCP4wiki (and XDSwiki).
It had been closed since we were hit by spammers (like e.g. PyMolwiki),
but we recently discovered a method that helps to prove that the account
is really created by a a human being - as opposed to a computer program
th
Dear All,
We have a great opportunity for somebody to join the structural biology
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Crystallograp
Dear Tim:
With the commend of "source /xtal/Suites/CCP4/ccp4-6.4.0/bin/ccp4.setup-sh",
I am able to run the xdsstat and f2mtz now.
Thank you very much for your help!
Uma
On Wed, Mar 12, 2014 at 5:42 AM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Uma,
>
> y
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Uma,
you have to run the command
source /xtal/Suites/CCP4/ccp4-6.4.0/bin/ccp4.setup-sh
in the terminal from which you start xdsstat (and f2mtz etc.pp). It is
best to place the above command into your file ~/.bashrc so that you
do not need to ty
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