Hi all
It might be a silly question but is there anyone who can explain what “peak-height z-value”, as well as “initial occupancy estimate” are in the file of “Mpro full XChem screen - hits summary - ver-2020-03-18”…
Thank you
Joshua
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Hi Joshua, good question. I’ll refer to the guys at Diamond @AnthonyA and @Daren_Fearon to answer this one.
Definitely one for @Daren_Fearon 
It is to do with the algorithm we use to find fragment hits in electron density maps Pandda. https://www.nature.com/articles/ncomms15123 and https://pandda.bitbucket.io/
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Hi Joshua,
As @AnthonyA says the Nat. Comm. paper will explain in more detail about the algorithm used in our pipeline.
In short, by using a set of related crystallographic data sets of the same crystal form we are able to calculate the Z-score (a measure of how significantly the data deviates from the average) at every point in space. This gives us a statistically meaningful measure for potentially interesting events such as a ligand binding. The larger the “peak-height z-value” the more significant the signal for a potential binding event is.
As ligand binding is rarely stoichiometric (particularly for low affinity compounds such as fragments) we refine the occupancy during our analysis and prepare an ensemble of bound and unbound states of the protein. However, only the bound states are shown in Fragalysis and currently deposited in the pdb. You can also read more on this here.
Hope that makes sense? If you have any other questions let me know.
Thank you very much! These papers definitely will help!
Thank you Daren! Your explanation is very important. Previously my guess is Z-value relates to the potency and I think I’m partially correct, I will do a further research. Thank you