Hi there,
I have a question regarding the interpretation of the last step of integrative modeling. I am wondering if the precision calculations (for structural clusters) presented in the analysis workflow (from PMI analysis repository on GitHub), will calculate precision for all components of the modeling system including the fixed rigid bodies? I am asking this as I have a good portion of my protein system being fixed in the modeling (for specific reasons), so I am not sure if that will impact the precision I get.
Thanks, Atefeh
On 9/25/20 3:13 PM, Atefeh Rafiei wrote: > I am wondering if the precision calculations (for > structural clusters) presented in the analysis workflow (from PMI > analysis repository on GitHub), will calculate precision for all > components of the modeling system including the fixed rigid bodies?
The shortest answer here is that you can't calculate sampling precision for something you didn't sample. So if your rigid bodies were not moved during the sampling, you should exclude them from the precision calculation, otherwise you'll get overly optimistic estimates for the precision.
The longer answer would depend on why you're fixing the rigid bodies in the first place.
Ben
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Atefeh Rafiei -
Ben Webb