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I have found that the best way to get the GAIN "right" in MOSFLM is to have a look at the optimum "Sdfac" parameter at the end of SCALA (the first of the three SDCORRection values). Specifically, if SDFac is > 1, then you need to increase the GAIN. This is because SDFac>1 means that the spots were noisier than MOSFLM thought they should be, and if a given number of ADU is noisier than expected, then there must have been fewer photons involved in generating the signal. This means that the "true gain" was higher. Yes, there are other sources of error, like shutter jitter, beam flicker, calibration errors, absorption effects, scale factor errors, etc. But these are all directly proportional to the intensity, and therefore accounted for by adjusting SDadd (the last of the three SDCORR values). SDfac accounts for noise proportional to the square root of intensity, and only shot noise (like photon counting) behaves like that. David Waterman makes an excellent point that the point-spread function (PSF) acts like a smoothing filter and makes the background look less noisy than photon-counting error permits. This makes the BGRATIO-estimated GAIN lower than the "true" GAIN. However, one can argue that this is not always a bad thing, since the error in measuring the intensity of a given area of flat background really is "better than photon counting". This is because you have the smoothing effect of the PSF working "for you": bringing in signal from areas outside the region you are measuring (prior knowledge of "flatness" if you will). However, this smoothing effect of the PSF does not apply to spots because spot photons all arrive in essentially the same place, and no "smoothing" will change the intrinsic noise of the total number of photons that actually arrived. The upshot of this is that we really need two different values for GAIN, one for the background and one for the background-subtracted spot intensity. The influence on sigma(I) would depend on the relative contributions from the spot vs the background under it. I am pretty sure this is not implemented. It is perhaps interesting that there is also a third type of noise which is independent of the spot intensity: "read-out noise". This used to be called "fog" on film detectors. Despite all the money we spend on detectors that minimize it, there is no specific accounting for read-out noise in MOSFLM or any other integration package I am aware of. However, a "trick" to account for it is to simply lower the ADCOFFSET. For example, using 1 A X-rays on an ADSC Q315r detector in hwbin mode, the true GAIN is 1.8 ADU/photon, the ADCOFFSET is 40 ADU, and the read-out noise is equivalent to the noise deposited by ~2 photon/pixel of x-ray background. This means that a blank image has an average value of 40 ADU and rms variation of ~2.5 ADU, but this is equivalent to an image from a detector with the same gain, no read-out noise, and ADCOFFSET of 36 that was "fogged" by 2 photons/pixel (regardless of exposure time). Yes, this is a small change in ADCOFFSET, and I doubt you will notice the difference. I think this speaks to the fact that, on modern detectors at least, read-out noise is essentially negligible. Another way to get the GAIN, of course, is to measure it directly. I did this on an ADSC Q315 detector in swbin mode by comparison to a NaI:Tl scintillator (after accounting for the window and sensor thickness of the latter device): http://bl831.als.lbl.gov/~jamesh/pickup/Q315_gain.png You can see how the GAIN changes appreciably with photon energy, and this is largely because lower-energy photons generate less signal. GAIN also changes with the detector read-out mode. For example, this number is 3 times higher for a Q315r in hwbin mode. I have listed my best information on the typical GAIN and read-out noise of common detectors on my "minimum crystal size" page here: http://bl831.als.lbl.gov/xtalsize.html You can extract the parameters by selecting the "detector type = " you want, and then switching it again to "Custom..." -James Holton MAD Scientist On 3/3/2011 12:34 PM, Bryan Lepore wrote: > wondering if mosflm can automatically estimate the gain. > > i.e. i gather it is still estimated the usual way. > > -Bryan