One more correction:
For example, if you see an average pixel value of 20 photons on a
Pilatus 6M, then that is P=120e6 photons. If that was a t=0.1 s
exposure from a sample 100 microns thick, then the beamline flux was
about 1e12 photons/s. Note that this is the flux after any attenuation,
Dear all,
we are in the editorial stages of a manuscript that I submitted to Wellcome
Open Research for publication.
The journal/editor ask us to list fully Open Source alternatives to the pieces
of software we used, for example for data processing and refinement.
What refinement programs are
Thank you Ethan for taking the the time to answer and explain.
Yes I am sure I have asked a vague and imprecise question.
Practically, I am going to point to xia2 for data processing:
https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Xia2/manual.html
and hope it is "Open Source enough" -
On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
> Dear all,
>
> we are in the editorial stages of a manuscript that I submitted to Wellcome
> Open Research for publication.
>
> The journal/editor ask us to list fully Open Source alternatives to the
> pieces of software we
Ah! I did that last formula wrong. Never do algebra in your head
without checking. It should be:
The equation then becomes:
f = P/t/L/1.2e-5
Where 1.2e-5 = 0.2 cm^2/g * 1.2 g/cm^3 * 1e-4 cm/micron * 50%, f=flux
and t=exposure (as above).
For example, if you see an average pixel value of
Could you point out where in this document the license is described?
While not particularly relevant to your question, TNT is a reasonable
example of what Ethan is talking about. TNT was always "open source"
since all source code was distributed to every user. It has never been
"free",
Hi Pietro,
To be precise, xia2 is a tool (which is open source under any definition - BSD
licensed) for running data processing programs on your behalf. If you run with
DIALS for indexing, integration and scaling (which are licensed the same way,
and uses cctbx which is also open source) then
On Thursday, 7 May 2020 10:18:38 PDT Roversi, Pietro (Dr.) wrote:
> Thank you Ethan for taking the the time to answer and explain.
> Yes I am sure I have asked a vague and imprecise question.
>
> Practically, I am going to point to xia2 for data processing:
>
Dear Pietro,
to add a bit to Ethan's warning, you might even consider XDS open
source: although the very source is not freely downloadable, it is so
well documented that one could rewrite the program just from its
documentation. At least, this is how the program SAINT started, as
far as I now.
Dear Ethan,
The copy of xia2 that I have on my machine says at the top of the source
> # Copyright (C) 2013 David Waterman
> #
> # This code is distributed under the terms and conditions of the
> # CCP4 Program Suite Licence Agreement as a CCP4 Application.
This surprised me
Hi Pietro!
As for free and open-source (GPLv3 license) refinement software, I am
developing Vagabond.
https://vagabond.hginn.co.uk
It is based on refining bond torsion angles in an ensemble of related
structures which also captures flexibility (no B factors!). There are no
restraints, only
Dear Tim,
While I agree that the papers describing XDS are excellent (and acknowledge
precisely this every time I talk about DIALS!) I am certain that the actual
implementation of XDS deviates significantly from the mathematical descriptions
in the paper for the simple reason that writing data
On Thursday, 7 May 2020 13:58:55 PDT David Waterman wrote:
> Dear Ethan,
>
> The copy of xia2 that I have on my machine says at the top of the source
> > # Copyright (C) 2013 David Waterman
> > #
> > # This code is distributed under the terms and conditions of the
> > # CCP4 Program
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