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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 09/2
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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: wh
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 wrote:
> Tim, I don't
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 wrote:
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> tg@slartibartfast:~/tmp$ phenix.python run.py
> 0.001 627.413-4.01639e+06
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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 2
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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
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 forma-factor
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Dear James,
Mann only fitted their data to sin\lambda/theta < 1.5, and up to there
the fit is pretty good. 30 years ago the computational means must have
been very different and what takes 5s now would have taken minutes or
hours then.
I am going to
That's really interesting! Since the fits then and now were both
least-squares, I wonder how Cromer & Mann could have gotten it so far
off? Looking at the residuals, I see that although that of nitrogen
oscillates badly, even the worst outlier is still within 0.01 electrons
of the Hartree-F
: Dienstag, 18. September 2012 15:32
An: Oliver Einsle
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Series termination effect calculation.
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Hello Oliver,
when you fit the values from ICA Tab 6.1.1.1 with gnuplot, the values of C and
N become much more
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Hello Oliver,
when you fit the values from ICA Tab 6.1.1.1 with gnuplot, the values
of C and N become much more comparable. c(C) = 0.017 and especially
c(N) = 0.025 > 0!!!
for C:
Final set of parametersAsymptotic Standard Error
===
Hi there,
I was just pointed to this thread and should comment on the discussion, as
actually made the plots for this paper. James has clarified the issue much
better than I could have, and indeed the calculations will fail for larger
Bragg angles if you do not assume a reasonable B-factor (I used
Tim,
Correct, but take care that 's' in Niu's program is
2.sin(theta)/lambda whereas in exp(-Bs^2) it is just sin(theta)/lambda
(as it is in the usual expression for f(s)).
Cheers
-- Ian
On 17 September 2012 10:24, Tim Gruene wrote:
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> Dear Ja
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Dear James et al.,
so to summarise, the answer to Niu's question is that he must add a
factor of e^(-Bs^2) to the formula of Cromer/Mann and then adjust the
value of B until it matches the inset. Given that you claim
rho=0.025e/A^3 (I assume for 1/dma
Le Lundi 17 Septembre 2012 08:32 CEST, James Holton a écrit
Hello
May I add a few words after the thorough comments by James.
I lmay be easier to consider series termination in real space as follows.
The effect of series termination in 3D on rho(r) is of convoluting the exact
rho(r) with the "
Yes, the constant term in the "5-Gaussian" structure factor tables does
become annoying when you try to plot electron density in real space, but
only if you try to make the B factor zero. If the B factors are ~12
(like they are in 1m1n), then the electron density 2.0 A from an Fe atom
is not -
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Dear Ian,
provided that f(s) is given by the formula in the Cromer/Mann article,
which I believe we have agreed on, the inset of Fig.1 of the Science
article we are talking about is claimed to be the graph of the
function g, which I added as pdf to th
On 14 September 2012 15:15, Tim Gruene wrote:
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> Hello Ian,
>
> your article describes f(s) as sum of four Gaussians, which is not the
> same f(s) from Cromer's and Mann's paper and the one used both by Niu
> and me. Here, f(s) contains a constant
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Hello Ian,
your article describes f(s) as sum of four Gaussians, which is not the
same f(s) from Cromer's and Mann's paper and the one used both by Niu
and me. Here, f(s) contains a constant, as I pointed out to in my
response, which makes the integra
On 14 September 2012 13:05, Tim Gruene wrote:
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> Dear Niu,
>
> as far as I can tell, all your parameters are correct and the
> scattering term for f(s) you use is also correct. f(s) furthermore
> matches very closely those tabulated in the Intl. T
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Dear Niu,
as far as I can tell, all your parameters are correct and the
scattering term for f(s) you use is also correct. f(s) furthermore
matches very closely those tabulated in the Intl. Tables C Tab. 6.1.1.1.
My reproduction of the mentioned formu
Hi,
pointers listed here may be of help:
1) CCP4 Newsletterhttp://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) https://www.phenix-online.org/presentations/latest/pavel_maps.pdf
3) Central
Dear Colleagues,
I am trying to repeat a series termination effect calculation displayed as
figure 2 in a publihsed paper
(http://www.ncbi.nlm.nih.gov/pubmed/12215645). Formula
(1) was used to implement this calculation. Since f(s) is not defined in
detail in this paper, I used formula and paramet
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