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 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 ([email protected]) 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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 ([email protected])

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

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 ([email protected])

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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