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Add support for Job plots #29
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Hey GuilIaume, I can volunteer to tackle the first task this weekend. For the other two, can you explain what you mean by the "best guess of the stoichiometry"? Are you referring to multiple ligand molecules binding to a single receptor? |
Hi @dododas ! Actually, I wrote this issue as a quick note/reminder, and I need to clarify a couple things. I think I would like to make a function for rapid plotting of a job plot (see https://en.wikipedia.org/wiki/Job_plot for the principle) and I think it will be easy. Maybe you already know the following, but I feel I need to explain a little bit. A Job plot aims at figuring out the stoichiometry, not the binding constant. Therefore, it requires a different experiment: instead of having molecule 1 at a fixed low concentration and a titration series of molecule 2, in a stoichiometry experiment the two molecules are titrated in opposite directions in a way that their molar fraction across the series will vary linearly, but the total concentration [molecule 1] + [molecule 2] will stay constant across the series. In this type of experiment, we need to follow a signal that is proportional to the amount of complex (which is the case of FRET) as a function of the molar fraction of one of the two molecules (usually, the one that we consider being the "receptor"). The resulting plot looks like a bell-shaped curve, where the maximum happens at the molar fraction that corresponds to the complex's stoichiometry (i.e. molar fraction of 0.5 if this is a 1:1 complex, molar fraction of 0.667 for a complex with two ligands per receptor, etc.). Since the concentration series in a stoichiometry experiment are linear, a log scale only distorts plots in a useless way. This is why I mentioned using a linear x scale, but I actually don't think we should modify I did some test experiments, and it turns out the Job plot looks similar whether I plot the raw or corrected FRET signal. The signal correction already works perfectly, it is simply a matter of naming columns in the input file appropriately. I hope I answered your questions. Please make sure you retrieve my latest commits in your branch before doing anything: I changed a lot of things in the past few weeks. Thanks for contributing! :-) |
Essentially done with #30. |
Current function |
This simply requires the following:
inspect_raw_data
should return all plots with linear x scales;The text was updated successfully, but these errors were encountered: