Add exp bi00595a029 2026 - #391
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| REAGENT_SOURCES: | ||
| DPPC: Synthesized locally, specifically deuterated at the choline alpha (+NCD2CH2-DPPC), beta (+NCH2CD2-DPPC), and gamma ((CD3)3N+-DPPC) segments | ||
| cholesterol: Purchased from Fluka, Switzerland | ||
| water: 0.2 M sodium acetate-acetic acid buffer (pH 5.7) with 10^-4 M EDTA |
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separately water, EDTA, acetic acid, soidum acetate
| PH: 5.7 | ||
| ADDITIONAL_MOLECULES: | ||
| EDTA: Ethylenediaminetetraacetic acid, 0.0001 M | ||
| Acetic_acid: sodium acetate-acetic acid, 0.2 M |
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I think, we can put NaCH3COO at 200mM to SOLUTION_COMPOSITION. It's almost that at this pH (I think). And Acetate anion is OK to add as actual read anion. Please add acetate molecule.
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@comcon1: So just to be clear, you would prefer NaCH3COO to be added as an actual molecule, because there is so much of it, correct? (Enough that it should probably be included on a precise simulation.)
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Of course. Look to the file: it's 200 milliM. It's a lot. It must be included. I think we include this amount of ions always. And also you cannot include a cation while not including the anion.
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I agree that 200 mM should be added. But, say, 1 mM can be, but should not be required.
Do we have a recommended limit above which an actual molecule should be added? If we don't have it yet, then would, say, 50 mM work?
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We can say, it's 50 mM can be recommended for small ions. Boundary mass % should also be named to consider size of an ion. I would recommend to consider the affinity: if it's Gd3+, even smaller amount must be added, if it's an anion the boundary could be higher. I don't see right now how to formulate strict rules, just recommendations.
I opened the issue NMRLipids/FAIRMD_lipids#501
| MOLAR_FRACTIONS: | ||
| DPPC: 1 | ||
| ION_CONCENTRATIONS: | ||
| SOD: 0.23 |
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Should we use mass-% also for the ION_CONCENTRATIONS? Or molarities?
The instructions for adding experimental data do not discuss this, probably because these are "outdated fields"? —> Should we actually just leave them out completely?
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For outdated fields, you should use outdated instructions. It were molarities there so it is molarities here.
We must leave them out completely after we complete changing the core code to complete pairing via only new fields. However, some development is missing for that. Now, the outdated fields should be saved otherwise the databank will not work.
| DPPC: 1 | ||
| SOLUTION_COMPOSITION: | ||
| SOD: 0.23 | ||
| Acetat-ion: 0.59 |
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This is not enough. Adding a molecule is a separate thing. Please read the documentation about molecule addition here:
https://nmrlipids.github.io/FAIRMD_lipids/stable/contrib/addingMolecule.html
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Closed as outdated duplicate of #405 |
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