RAW series vs chromixs for SEC SAXS

[Pernille sønderby]

Hi Jesse,

I have data from a SEC SAXS run and as chromixs from Atsas has a weird issue on my computer I moved to RAW.

I have the wirdest thing happening. I have attached a picture. The same data displys very differently in the two programs.

I am gussing it has to do with the averaging of the files. But how to fix it?

Best Pernille

[Richard Gillilan]

In RAW, make sure you have normalization (beamstop diode or via direct spot on detector) turned on if you are reading detector images directly (as opposed to reading in .dat files that are already normalized). RAW reads detector images, then looks for the counter file to apply beamstop normalization (they way we do it as CHESS).

Also, in RAW you can choose to display different types of plot. The default is total integrated intensity, but you can also display intensity at a single q or integrated over a q range. Sometimes integrating over a q limited range helps because you can leave out some of the low-q data ... for example integrate over 0.02 to 0.4 ... very low q can flicker as synchrotron beam position may vary a little over short timescale. In doing that, the actual height of the peaks at low q may change.

I don't know how chromixs processes the data. It is interesting to see the comparison.

Richard

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[Richard Gillilan]

I also notice that chromixs plots something called "average intensity." I wonder if that is the same as "integrated intensity" or if they do something different?

On Jun 16, 2023, at 4:12 AM, Pernille sønderby <pernille...@gmail.com> wrote:

[Jesse Hopkins]

Hi Pernille,

By default CHROMIXS displays the average intensity between 0.01 and 0.08 1/A. This is a range that tends to have relatively strong protein signal, and so this can be useful for reducing the overall noise in the intensity vs. frame number display. By default, RAW displays the total intensity across the entire q range of the dataset. This helps make sure that you don’t miss changes in the data due to things like accumulating radiation damage changing the low q values or a drift in the high q values due to beam motion, but leads to more noise in the intensity vs. frame number display. Basically, there’s tradeoffs either way.

If you want to display something essentially equivalent to CHROMIXS, right click on the series plot, go to the “Y Data (Left Axis)” sub menu, and select “Intensity in q range”. Then enter “0.01, 0.08” (without the quotes) and click OK. That will display something very similar to the CHROMIXS plot (RAW will be displaying total intensity and CHROMIXS will display average intensity, but overall it will look basically the same). See attached screenshots.

Let me know if that does the trick for you.

To Richard’s point about images, CHROMIXS only works with .dat files, so you don’t have to worry about that here.

All the best.

- Jesse

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Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

To view this discussion on the web visit https://groups.google.com/d/msgid/bioxtas_raw/D9C4772E-2070-459E-92D7-08FC59B822D3%40cornell.edu.

[Pernille sønderby]

Hi Jesse and Richard,

I did get it working similar to Chromixs. It is simply confusing to see data so differently shown, than at the synchrotron:) 

I do find RAW has a lot more capabilities though, and use RAW on a daily basis as well. I will use this chance as well to thank you for the ease of output with the analysis data. The analysis file is so easy to work with in python and just make table making and plotting a lot sweeter. 

Thank you very much for your help.
Best regards

Pernille