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BranniganLab / density_threshold_affinity

Scripts to Assist Density Threshold Affinity Analysis - a method for obtaining free energies of protein-lipid binding. Originally described in: https://pubs.aip.org/aip/jcp/article/154/18/185102/200265/Spontaneous-lipid-binding-to-the-nicotinic and subsequently refined in: https://doi.org/10.1016/bs.mie.2024.03.008
https://doi.org/10.1016/bs.mie.2024.03.008
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README suggestions and clarification #57

Open lms464 opened 3 months ago

lms464 commented 3 months ago

For Step 2, I want to suggest

I am running, conda 24.1.2 on a 24.04 ubuntu laptop, and when I used the command provided below, it created a conda environment lacking python --

[Optional:] conda create -n DTA

I want to suggest changing it to--

[Optional:] conda create -n DTA python=3.X.X

Personally I would push to make the #[Optional:] components mandatory to avoid version changes to new users' other libraries. Another option is Docker, but that may be too extreme.

Seems to be a known issue but -- Step 9. I opened plot_enrichment, polarDensity_helper is called, but it is not a known file/library. Looking at the DTA.ipynb, I think this needs to be changed to from DTA import....

JesseSandberg commented 3 months ago

Need to update the "manuscript currently in prep" line too with DOI: https://doi.org/10.1016/bs.mie.2024.03.008