[phenixbb] Units in intensity?

[Tim Gruene]

Dear Peligro,

this formula has little meaning for diffraction intensities, I would guess. 
First of all, reflections usually cover several pixel on your detector, 
especially on CCDs. Secondly, integration software goes to great strength to 
extract a crystallographically meaningful signal from the detector. This 
includes subtraction of a background estimate, and profile fitting at least for 
the weaker reflections. Finally, the sigma-value in your final data file has an 
error model applied that corrects for systematic errors. This is quite 
different and usually much higher (about an order of magnitude) than the sigma-
value from counting statistics.

So please use this with care.

Best regards,
Tim


On Thursday, March 7, 2019 9:05:46 PM CET Murpholino Peligro wrote:
> I got from here http://webhome.phy.duke.edu/~kolena/hou/counts.html a
> formula for the number of counts (c=faqt; where c is the number of counts,
> f is the photon flux, a is the area, q is the quantum efficiency and t is
> the exposure time) It is for telescopes but I guess is not a lot different
> for the detector used in xrc.
> 
> Thank you very much.
> 
> 
> 
> El mié., 6 de mar. de 2019 a la(s) 19:20, Johan Hattne (hattne at ucla.edu)
> 
> escribió:
> > I think that would depend on how the detector is measuring the photons
> > that impinge on it.
> > 
> > Unless you’re actually concerned with exactly how the detector does its
> > thing, I think Tim’s dimensionless or something fuzzy like “detector unit”
> > is fine.
> > 
> > // Johan
> > 
> > > On Mar 6, 2019, at 14:16, Murpholino Peligro <murpholinox at gmail.com>
> > 
> > wrote:
> > > ...
> > > The counts are the number of x-ray photons converted to electrons?
> > > 
> > > 
> > > Thanks
> > > 
> > > El mié., 6 de mar. de 2019 a la(s) 15:18, Tim Gruene (tim.gruene at psi.ch)
> > 
> > escribió:
> > > Dear Murpholino,
> > > 
> > > the unit of intensity is '1' - it is the counts on the detector. The
> > 
> > scale is
> > 
> > > arbitrary, you can multiply your intensity with any positive number you
> > 
> > want,
> > 
> > > as long as you don't create an overflow or underflow in the computer
> > 
> > program.
> > 
> > >  As long as you do the same with the sigma-values, your refinement
> > 
> > should not
> > 
> > > change.
> > > 
> > > Best regards,
> > > Tim
> > > 
> > > On Wednesday, March 6, 2019 10:00:55 PM CET Murpholino Peligro wrote:
> > > > If I do `phenix.xtriage XDS_ASCII.HKL` I get a log file. In the
> > 
> > "Statistics
> > 
> > > > for data merging" of this log file I have:
> > > >     Resolution: 26.02 - 1.40
> > > >     Observations: 44675
> > > >     Unique reflections: 16306
> > > >     Redundancy: 2.7
> > > >     Completeness: 70.37%
> > > >     Mean intensity: 1656.8
> > > >     Mean I/sigma(I): 19.8
> > > >     SigI < 0 (rejected): 644 observations
> > > >     R-merge: 0.027
> > > >     R-meas:  0.032
> > > >     R-pim:   0.017
> > > > 
> > > > My question is... what units does Mean intensity has?
> > > > 
> > > > Thanks
> > > > Ps I am not sure if this has to do with the detector used which was a
> > 
> > CCD
> > 
> > > > (type) ADSC QUANTUM 210 (model).
> > > 
> > > --
> > > --
> > > Tim Gruene
> > > Head of the Centre for X-ray Structure Analysis
> > > Faculty of Chemistry
> > > University of Vienna
> > > 
> > > Phone: +43-1-4277-70202
> > > 
> > > GPG Key ID = A46BEE1A
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> >           Research Specialist @ Gonen Lab
> > 
> > ____________________________________________________
> > 
> >       UCLA * 615 Charles E. Young Drive South
> >       
> >          BSRB #347 * Los Angeles, CA 90095

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A
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